openapi: 3.0.3 info: title: Girder REST API (Emory Digital Slide Archive) version: 3.2.14 description: OpenAPI 3.0 conversion of the Girder REST API powering the Emory Digital Slide Archive (computablebrain). Converted faithfully from the live Swagger 2.0 document at https://computablebrain.emory.edu/api/v1/describe. license: name: Apache-2.0 url: https://www.apache.org/licenses/LICENSE-2.0.txt servers: - url: https://computablebrain.emory.edu/api/v1 tags: - description: annotation resource name: annotation - description: api_key resource name: api_key - description: assetstore resource name: assetstore - description: collection resource name: collection - description: dicomweb_assetstore resource name: dicomweb_assetstore - description: file resource name: file - description: files resource name: files - description: folder resource name: folder - description: group resource name: group - description: histomicsui resource name: histomicsui - description: homepage resource name: homepage - description: item resource name: item - description: job resource name: job - description: large_image resource name: large_image - description: notification resource name: notification - description: resource resource name: resource - description: slicer_cli_web resource name: slicer_cli_web - description: system resource name: system - description: tcga resource name: tcga - description: token resource name: token - description: user resource name: user - description: worker resource name: worker paths: /annotation: get: operationId: annotation_find_annotation parameters: - name: itemId in: query required: false description: List all annotations in this item. schema: type: string - name: userId in: query required: false description: List all annotations created by this user. schema: type: string - name: text in: query required: false description: Pass this to perform a full text search for annotation names and descriptions. schema: type: string - name: name in: query required: false description: Pass to lookup an annotation by exact name match. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lowerName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Annotation' '400': description: A parameter was invalid. '403': description: Read access was denied on the parent item. summary: Search for annotations. tags: - annotation post: operationId: annotation_createAnnotation_post_annotation parameters: - name: itemId in: query required: true description: The ID of the associated item. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Annotation' '400': description: 'ID was invalid. Invalid JSON passed in request body. Validation Error: JSON doesn''t follow schema.' '403': description: Read access was denied for the item. summary: Create an annotation. tags: - annotation requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the annotation. /annotation/counts: get: operationId: annotation_getItemListAnnotationCounts_counts parameters: - name: items in: query required: true description: A comma-separated list of item ids. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get annotation counts for a list of items. If using actual a database other than DocumentDB, this also indicates if items are referenced as annotations. tags: - annotation /annotation/folder/{id}: delete: operationId: annotation_deleteFolderAnnotations_delete_folder_id parameters: - name: id in: path required: true description: The ID of the folder schema: type: string - name: recurse in: query required: false description: Whether or not to retrieve all annotations from subfolders schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. summary: Delete all user-owned annotations from the items in a folder tags: - annotation get: operationId: annotation_returnFolderAnnotations_folder_id parameters: - name: id in: path required: true description: The ID of the folder schema: type: string - name: recurse in: query required: false description: Whether or not to retrieve all annotations from subfolders schema: type: boolean default: false - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: created - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Get the user-owned annotations from the items in a folder tags: - annotation /annotation/folder/{id}/access: put: operationId: annotation_setFolderAnnotationAccess_put_folder_id_access parameters: - name: id in: path required: true description: The ID of the folder schema: type: string - name: access in: query required: true description: The JSON-encoded access control list. schema: type: string - name: public in: query required: false description: Whether the annotation should be publicly visible. schema: type: boolean - name: recurse in: query required: false description: Whether or not to retrieve all annotations from subfolders schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. summary: Set the access for all the user-owned annotations from the items in a folder tags: - annotation /annotation/folder/{id}/create: get: operationId: annotation_canCreateFolderAnnotations_folder_id_create parameters: - name: id in: path required: true description: The ID of the folder schema: type: string responses: '200': description: Success '400': description: ID was invalid. summary: Check if the user can create annotations in a folder tags: - annotation /annotation/folder/{id}/present: get: operationId: annotation_existFolderAnnotations_folder_id_present parameters: - name: id in: path required: true description: The ID of the folder schema: type: string - name: recurse in: query required: false description: Whether or not to recursively check subfolders for annotations schema: type: boolean default: true responses: '200': description: Success '400': description: A parameter was invalid. summary: Check if the user owns any annotations for the items in a folder tags: - annotation /annotation/images: get: description: By default, this endpoint will return a list of recently annotated images. This list can be further filtered by passing the creatorId and/or imageName parameters. The creatorId parameter will limit results to annotations created by the given user. The imageName parameter will only include images whose name (or a token in the name) begins with the given string. operationId: annotation_findAnnotatedImages_images parameters: - name: creatorId in: query required: false description: Limit to annotations created by this user schema: type: string - name: imageName in: query required: false description: Filter results by image name (case-insensitive) schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: updated - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Search for annotated images. tags: - annotation /annotation/item/{id}: delete: description: This deletes all annotation model records. operationId: annotation_deleteItemAnnotations_delete_item_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the item. summary: Delete all annotations for an item. tags: - annotation get: description: This returns a list of annotation model records. operationId: annotation_getItemAnnotations_item_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get all annotations for an item. tags: - annotation post: operationId: annotation_createItemAnnotations_post_item_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: 'ID was invalid. Invalid JSON passed in request body. Validation Error: JSON doesn''t follow schema.' '403': description: Write access was denied for the item. summary: Create multiple annotations on an item. tags: - annotation requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON list of annotation model records or annotations. If these are complete models, the value of the "annotation" key is used and the other information is ignored (such as original creator ID). /annotation/item/{id}/plot/data: post: operationId: annotation_getItemPlottableData_post_item_id_plot_data parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: adjacentItems in: query required: false description: Whether to include adjacent item data. schema: type: string enum: - 'false' - 'true' - __all__ default: false - name: keys in: query required: true description: A comma separated list of data keys to retrieve (not json). schema: type: string - name: requiredKeys in: query required: false description: A comma separated list of data keys that must be non null in all response rows (not json). schema: type: string - name: sources in: query required: false description: An optional comma separated list that can contain folder, item, annotation, annotationelement, datafile. schema: type: string - name: uuid in: query required: false description: An optional uuid to allow cancelling a previous request. If specified and there are any outstanding requests with the same uuid, they may be cancelled to save resources. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get plottable data related to an item and its annotations. tags: - annotation requestBody: content: multipart/form-data: schema: type: object properties: annotations: type: string description: A JSON list of annotation IDs that should be included. An entry of \__all__ will include all annotations. compute: type: string description: 'A dictionary with keys "columns": a list of columns to include in the computation; if unspecified or an empty list, no computation is done, "function": a string with the name of the function, such as umap, "params": additional parameters to pass to the function. If none of the requiredKeys are compute.(x|y|z), the computation will not be performed. Only rows which have all selected columns present will be included in the computation.' /annotation/item/{id}/plot/list: post: operationId: annotation_getItemPlottableElements_post_item_id_plot_list parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: adjacentItems in: query required: false description: Whether to include adjacent item data. schema: type: string enum: - 'false' - 'true' - __all__ default: false - name: sources in: query required: false description: An optional comma separated list that can contain folder, item, annotation, annotationelement, datafile. schema: type: string - name: uuid in: query required: false description: An optional uuid to allow cancelling a previous request. If specified and there are any outstanding requests with the same uuid, they may be cancelled to save resources. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a list of plottable data related to an item and its annotations. tags: - annotation requestBody: content: multipart/form-data: schema: type: object properties: annotations: type: string description: A JSON list of annotation IDs that should be included. An entry of \__all__ will include all annotations. /annotation/old: delete: operationId: annotation_deleteOldAnnotations_delete_old parameters: - name: age in: query required: false description: The minimum age in days. schema: type: integer format: int32 default: 30 - name: versions in: query required: false description: Keep at least this many history entries for each annotation. schema: type: integer format: int32 default: 10 responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete old annotations. tags: - annotation get: operationId: annotation_getOldAnnotations_old parameters: - name: age in: query required: false description: The minimum age in days. schema: type: integer format: int32 default: 30 - name: versions in: query required: false description: Keep at least this many history entries for each annotation. schema: type: integer format: int32 default: 10 responses: '200': description: Success '400': description: A parameter was invalid. summary: Report on old annotations. tags: - annotation /annotation/schema: get: description: In addition to the schema, if IDs are specified on elements, all IDs must be unique. operationId: annotation_getAnnotationSchema_schema responses: '200': description: Success '400': description: A parameter was invalid. summary: Get the official Annotation schema tags: - annotation parameters: [] /annotation/{id}: delete: operationId: annotation_deleteAnnotation_delete_id parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the annotation. summary: Delete an annotation. tags: - annotation get: description: Use "size" or "details" as possible sort keys. operationId: annotation_getAnnotation_id parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: left in: query required: false description: The left column of the area to fetch. schema: type: number format: float - name: right in: query required: false description: The right column (exclusive) of the area to fetch. schema: type: number format: float - name: top in: query required: false description: The top row of the area to fetch. schema: type: number format: float - name: bottom in: query required: false description: The bottom row (exclusive) of the area to fetch. schema: type: number format: float - name: low in: query required: false description: The lowest z value of the area to fetch. schema: type: number format: float - name: high in: query required: false description: The highest z value (exclusive) of the area to fetch. schema: type: number format: float - name: minimumSize in: query required: false description: Only annotations larger than or equal to this size in pixels will be returned. Size is determined by the length of the diagonal of the bounding box of an element. This probably should be 1 at the maximum zoom, 2 at the next level down, 4 at the next, etc. schema: type: number format: float - name: maxDetails in: query required: false description: Limit the number of annotations returned based on complexity. The complexity of an annotation is how many points are used to defined it. This is applied in addition to the limit. Using maxDetails helps ensure results will be able to be rendered. schema: type: integer format: int32 - name: minElements in: query required: false description: If maxDetails is specified, always return at least this many elements, even if they are very detailed. schema: type: integer format: int32 - name: centroids in: query required: false description: If true, only return the centroids of each element. The results are returned as a packed binary array with a json wrapper. schema: type: boolean - name: bbox in: query required: false description: If true, add _bbox records to each element. These are computed when the annotation is stored and cannot be modified. Cannot be used with the centroids option. schema: type: boolean - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _id - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the annotation. summary: Get an annotation by id. tags: - annotation patch: operationId: annotation_patchAnnotation_patch_id parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string responses: '200': description: Success '204': description: No Content; the annotation was successfully updated but is not returned '400': description: 'Invalid JSON passed in request body. Validation Error: JSON doesn''t follow schema.' '403': description: Write access was denied for the item. summary: Patch an annotation or its elements. tags: - annotation requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the annotation patch. This is a list. Each entry is an operation that contains "op", "path", and possibly "value". "op" can be any of "replace", "add", or "remove". "path" is either a root property (e.g., "name"), or "elements/id:{element id}". Any path to a dictionary or list can be extended via .../(key or index) components. Add and replace operations must include the value. put: operationId: annotation_updateAnnotation_put_id parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: itemId in: query required: false description: Pass this to move the annotation to a new item. schema: type: string responses: '200': description: Success '400': description: 'Invalid JSON passed in request body. Validation Error: JSON doesn''t follow schema.' '403': description: Write access was denied for the item. summary: Update an annotation or move it to a different item. tags: - annotation requestBody: content: application/json: schema: $ref: '#/components/schemas/string' description: A JSON object containing the annotation. If the "annotation":"elements" property is not set, the elements will not be modified. /annotation/{id}/access: get: operationId: annotation_getAnnotationAccess_id_access parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin access was denied for the annotation. summary: Get the access control list for an annotation. tags: - annotation put: operationId: annotation_updateAnnotationAccess_put_id_access parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: access in: query required: true description: The JSON-encoded access control list. schema: type: string - name: public in: query required: false description: Whether the annotation should be publicly visible. schema: type: boolean responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin access was denied for the annotation. summary: Update the access control list for an annotation. tags: - annotation /annotation/{id}/copy: post: operationId: annotation_copyAnnotation_post_id_copy parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: itemId in: query required: true description: The ID of the destination item. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the item. summary: Copy an annotation from one item to an other. tags: - annotation /annotation/{id}/history: get: operationId: annotation_getAnnotationHistoryList_id_history parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 0 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _version - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '403': description: Read access was denied for the annotation. summary: Get a list of an annotation's history. tags: - annotation /annotation/{id}/history/revert: put: description: This can be used to undelete an annotation by reverting to the most recent version. operationId: annotation_revertAnnotationHistory_put_id_history_revert parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: version in: query required: false description: The version of the annotation. If not specified, if the annotation was deleted this undeletes it. If it was not deleted, this reverts to the previous version. schema: type: integer format: int32 responses: '200': description: Success '400': description: Annotation history version not found. '403': description: Read access was denied for the annotation. summary: Revert an annotation to a specific version. tags: - annotation /annotation/{id}/history/{version}: get: operationId: annotation_getAnnotationHistory_id_history_version parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: version in: path required: true description: The version of the annotation. schema: type: integer format: int32 responses: '200': description: Success '400': description: Annotation history version not found. '403': description: Read access was denied for the annotation. summary: Get a specific version of an annotation's history. tags: - annotation /annotation/{id}/metadata: delete: operationId: annotation_deleteMetadata_delete_id_metadata parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the annotation. summary: Delete metadata (annotation.attributes) fields on an annotation. tags: - annotation requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON list containing the metadata fields to delete put: description: Set metadata fields to null in order to delete them. operationId: annotation_setMetadata_put_id_metadata parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: allowNull in: query required: false description: Whether "null" is allowed as a metadata value. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Annotation' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the annotation. summary: Set metadata (annotation.attributes) fields on an annotation. tags: - annotation requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata keys to add /annotation/{id}/{format}: get: description: Use "size" or "details" as possible sort keys. operationId: annotation_getAnnotationWithFormat_id_format parameters: - name: id in: path required: true description: The ID of the annotation. schema: type: string - name: format in: path required: true description: The format of the annotation. schema: type: string enum: - geojson responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the annotation. summary: Get an annotation by id in a specific format. tags: - annotation /api_key: get: description: Only site administrators may list keys for other users. If no userId parameter is passed, lists keys for the current user. operationId: api_key_listKeys_api_key parameters: - name: userId in: query required: false description: ID of the user whose keys to list. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List API keys for a given user. tags: - api_key post: operationId: api_key_createKey_post_api_key parameters: - name: name in: query required: false description: Name for the API key. schema: type: string default: '' - name: scope in: query required: false description: JSON list of scopes for this key. schema: type: string - name: tokenDuration in: query required: false description: Max number of days tokens created with this key will last. schema: type: string - name: active in: query required: false description: Whether the key is currently active. schema: type: boolean default: true - name: targetUserId in: query required: false description: Id of user to apply the key to schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Create a new API key. tags: - api_key /api_key/token: post: operationId: api_key_createToken_post_token parameters: - name: key in: query required: true description: The API key. schema: type: string - name: duration in: query required: false description: Number of days that the token should last. schema: type: number format: float responses: '200': description: Success '400': description: A parameter was invalid. summary: Create a token from an API key. tags: - api_key /api_key/{id}: delete: operationId: api_key_deleteKey_delete_id parameters: - name: id in: path required: true description: The ID of the API key to delete. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete an API key. tags: - api_key put: operationId: api_key_updateKey_put_id parameters: - name: id in: path required: true description: The ID of the API key. schema: type: string - name: name in: query required: false description: Name for the key. schema: type: string - name: scope in: query required: false description: JSON list of scopes for this key. schema: type: string default: [] - name: tokenDuration in: query required: false description: Max number of days tokens created with this key will last. schema: type: string - name: active in: query required: false description: Whether the key is currently active. schema: type: boolean responses: '200': description: Success '400': description: A parameter was invalid. summary: Update an API key. tags: - api_key /assetstore: get: operationId: assetstore_find_assetstore parameters: - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: List assetstores. tags: - assetstore post: description: You must be an administrator to call this. operationId: assetstore_createAssetstore_post_assetstore parameters: - name: name in: query required: true description: Unique name for the assetstore. schema: type: string - name: type in: query required: true description: Type of the assetstore. schema: type: integer format: int32 - name: root in: query required: false description: Root path on disk (for filesystem type). schema: type: string - name: perms in: query required: false description: File creation permissions (for filesystem type). schema: type: string - name: db in: query required: false description: Database name (for GridFS type) schema: type: string - name: mongohost in: query required: false description: Mongo host URI (for GridFS type) schema: type: string - name: replicaset in: query required: false description: Replica set name (for GridFS type) schema: type: string - name: bucket in: query required: false description: The S3 bucket to store data in (for S3 type). schema: type: string - name: prefix in: query required: false description: Optional path prefix within the bucket under which files will be stored (for S3 type). schema: type: string default: '' - name: accessKeyId in: query required: false description: The AWS access key ID to use for authentication (for S3 type). schema: type: string - name: secret in: query required: false description: The AWS secret key to use for authentication (for S3 type). schema: type: string - name: service in: query required: false description: The S3 service host (for S3 type). Default is s3.amazonaws.com. This can be used to specify a protocol and port as well using the form [http[s]://](host domain)[:(port)]. Do not include the bucket name here. schema: type: string default: '' - name: readOnly in: query required: false description: If this assetstore is read-only, set this to true. schema: type: boolean default: false - name: region in: query required: false description: The AWS region to which the S3 bucket belongs. schema: type: string default: us-east-1 - name: inferCredentials in: query required: false description: The credentials for connecting to S3 will be inferred by Boto rather than explicitly passed. Inferring credentials will ignore accessKeyId and secret. schema: type: boolean - name: serverSideEncryption in: query required: false description: Whether to use S3 SSE to encrypt the objects uploaded to this bucket (for S3 type). schema: type: boolean default: false - name: allowS3AcceleratedTransfer in: query required: false description: Whether to allow clients to requests a data transfer using S3 transfer acceleration. schema: type: boolean default: false - name: url in: query required: false description: The base URL for the DICOMweb server (for DICOMweb) schema: type: string - name: qido_prefix in: query required: false description: The QIDO URL prefix for the server, if needed (for DICOMweb) schema: type: string - name: wado_prefix in: query required: false description: The WADO URL prefix for the server, if needed (for DICOMweb) schema: type: string - name: auth_type in: query required: false description: The authentication type required for the server, if needed (for DICOMweb) schema: type: string - name: auth_token in: query required: false description: Token for authentication if needed (for DICOMweb) schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Assetstore' '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: Create a new assetstore. tags: - assetstore /assetstore/all_imports: get: operationId: assetstore_listAllImports_all_imports parameters: - name: unique in: query required: false description: If true, only show unique imports schema: type: boolean default: false - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: started - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List all past imports for all assetstores. tags: - assetstore /assetstore/import/{id}: get: operationId: assetstore_getImport_import_id parameters: - name: id in: path required: true description: ID of an import schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get import for record from ID. tags: - assetstore /assetstore/{id}: delete: description: This will fail if there are any files in the assetstore. operationId: assetstore_deleteAssetstore_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: 'A parameter was invalid. The assetstore is not empty.' '403': description: You are not an administrator. summary: Delete an assetstore. tags: - assetstore get: operationId: assetstore_getAssetstore_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: Get information about an assetstore. tags: - assetstore put: operationId: assetstore_updateAssetstore_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: query required: true description: Unique name for the assetstore. schema: type: string - name: root in: query required: false description: Root path on disk (for Filesystem type) schema: type: string - name: perms in: query required: false description: File creation permissions (for Filesystem type) schema: type: string - name: db in: query required: false description: Database name (for GridFS type) schema: type: string - name: mongohost in: query required: false description: Mongo host URI (for GridFS type) schema: type: string - name: replicaset in: query required: false description: Replica set name (for GridFS type) schema: type: string - name: bucket in: query required: false description: The S3 bucket to store data in (for S3 type). schema: type: string - name: prefix in: query required: false description: Optional path prefix within the bucket under which files will be stored (for S3 type). schema: type: string default: '' - name: accessKeyId in: query required: false description: The AWS access key ID to use for authentication (for S3 type). schema: type: string - name: secret in: query required: false description: The AWS secret key to use for authentication (for S3 type). schema: type: string - name: service in: query required: false description: The S3 service host (for S3 type). Default is s3.amazonaws.com. This can be used to specify a protocol and port as well using the form [http[s]://](host domain)[:(port)]. Do not include the bucket name here. schema: type: string default: '' - name: readOnly in: query required: false description: If this assetstore is read-only, set this to true. schema: type: boolean - name: region in: query required: false description: The AWS region to which the S3 bucket belongs. schema: type: string default: us-east-1 - name: current in: query required: true description: Whether this is the current assetstore schema: type: boolean - name: inferCredentials in: query required: false description: The credentials for connecting to S3 will be inferred by Boto rather than explicitly passed. Inferring credentials will ignore accessKeyId and secret. schema: type: boolean - name: serverSideEncryption in: query required: false description: Whether to use S3 SSE to encrypt the objects uploaded to this bucket (for S3 type). schema: type: boolean default: false - name: allowS3AcceleratedTransfer in: query required: false description: Whether to allow clients to requests a data transfer using S3 transfer acceleration. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Assetstore' '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: Update an existing assetstore. tags: - assetstore /assetstore/{id}/files: get: operationId: assetstore_getAssetstoreFiles_id_files parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _id - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: Get a list of files controlled by an assetstore. tags: - assetstore /assetstore/{id}/import: post: description: This does not move or copy the existing data, it just creates references to it in the Girder data hierarchy. Deleting those references will not delete the underlying data. This operation is currently only supported for S3 assetstores. operationId: assetstore_importDataWrapper_post_id_import parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: importPath in: query required: false description: Root path within the underlying storage system to import. schema: type: string - name: destinationId in: query required: true description: ID of a folder, collection, or user in Girder under which the data will be imported. schema: type: string - name: destinationType in: query required: true description: Type of the destination resource. schema: type: string enum: - folder - collection - user - name: progress in: query required: false description: Whether to record progress on the import. schema: type: boolean default: false - name: leafFoldersAsItems in: query required: false description: Whether folders containing only files should be imported as items. schema: type: boolean default: false - name: fileIncludeRegex in: query required: false description: If set, only filenames matching this regular expression will be imported. schema: type: string - name: fileExcludeRegex in: query required: false description: If set, only filenames that do not match this regular expression will be imported. If a file matches both the include and exclude regex, it will be excluded. schema: type: string - name: excludeExisting in: query required: false description: If true, then a file with an import path that is already in the system is not imported, even if it is not in the destination hierarchy. schema: type: boolean default: false responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: Import existing data into an assetstore. tags: - assetstore /assetstore/{id}/import/single_path: post: operationId: assetstore_importSinglePath_post_id_import_single_path parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: itemId in: query required: true description: The ID of the document. schema: type: string - name: path in: query required: true description: The new import path of the file. schema: type: string - name: name in: query required: true description: The name to use for the file. schema: type: string - name: mimeType in: query required: false description: The mimetyoe of the file. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/File' '400': description: ID was invalid. '403': description: Write access was denied on the parent folder. summary: Import a single path into an assetstore. tags: - assetstore /assetstore/{id}/imports: get: operationId: assetstore_listImports_id_imports parameters: - name: id in: path required: true description: An assetstore ID schema: type: string - name: unique in: query required: false description: If true, only show unique imports schema: type: boolean default: false - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: started - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List all imports for a given assetstore. tags: - assetstore /collection: get: operationId: collection_find_collection parameters: - name: text in: query required: false description: Pass this to perform a text search for collections. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/Collection' type: array '400': description: A parameter was invalid. summary: List or search for collections. tags: - collection post: operationId: collection_createCollection_post_collection parameters: - name: name in: query required: true description: Name for the collection. Must be unique. schema: type: string - name: description in: query required: false description: Collection description. schema: type: string - name: public in: query required: false description: Whether the collection should be publicly visible. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Collection' '400': description: A parameter was invalid. '403': description: You are not authorized to create collections. summary: Create a new collection. tags: - collection /collection/details: get: operationId: collection_getCollectionsDetails_details responses: '200': description: Success '400': description: A parameter was invalid. summary: Get detailed information of accessible collections. tags: - collection parameters: [] /collection/{id}: delete: operationId: collection_deleteCollection_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin permission denied on the collection. summary: Delete a collection by ID. tags: - collection get: operationId: collection_getCollection_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Collection' '400': description: ID was invalid. '403': description: Read permission denied on the collection. summary: Get a collection by ID. tags: - collection put: operationId: collection_updateCollection_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: query required: false description: Unique name for the collection. schema: type: string - name: description in: query required: false description: Collection description. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Collection' '400': description: ID was invalid. '403': description: Write permission denied on the collection. summary: Edit a collection by ID. tags: - collection /collection/{id}/access: get: operationId: collection_getCollectionAccess_id_access parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin permission denied on the collection. summary: Get the access control list for a collection. tags: - collection put: operationId: collection_updateCollectionAccess_put_id_access parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: access in: query required: true description: The access control list as JSON. schema: type: string - name: publicFlags in: query required: false description: List of public access flags to set on the collection. schema: type: string - name: public in: query required: false description: Whether the collection should be publicly visible. schema: type: boolean - name: recurse in: query required: false description: Whether the policies should be applied to all folders under this collection as well. schema: type: boolean default: false - name: progress in: query required: false description: If recurse is set to True, this controls whether progress notifications will be sent. schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin permission denied on the collection. summary: Set the access control list for a collection. tags: - collection /collection/{id}/details: get: operationId: collection_getCollectionDetails_id_details parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the collection. summary: Get detailed information about a collection. tags: - collection /collection/{id}/download: get: operationId: collection_downloadCollection_id_download parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: mimeFilter in: query required: false description: JSON list of MIME types to include. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the collection. summary: Download an entire collection as a zip archive. tags: - collection /collection/{id}/metadata: delete: operationId: collection_deleteMetadata_delete_id_metadata parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Collection' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the collection. summary: Delete metadata fields on a collection. tags: - collection requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON list containing the metadata fields to delete put: description: Set metadata fields to null in order to delete them. operationId: collection_setMetadata_put_id_metadata parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: allowNull in: query required: false description: Whether "null" is allowed as a metadata value. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Collection' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the collection. summary: Set metadata fields on a collection. tags: - collection requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata keys to add /collection/{id}/quota: get: operationId: collection_getCollectionQuota_id_quota parameters: - name: id in: path required: true description: The collection ID schema: type: string responses: '200': description: Success '400': description: ID was invalid. summary: Get quota and assetstore policies for the collection. tags: - collection put: operationId: collection_setCollectionQuota_put_id_quota parameters: - name: id in: path required: true description: The collection ID schema: type: string - name: policy in: query required: true description: A JSON object containing the policies. This is a dictionary of keys and values. Any key that is not specified does not change. schema: type: string responses: '200': description: Success '400': description: ID was invalid. summary: Set quota and assetstore policies for the collection. tags: - collection /dicomweb_assetstore/{id}/import: post: operationId: dicomweb_assetstore_importData_post_id_import parameters: - name: id in: path required: true description: The ID of the assetstore representing the DICOMweb server. schema: type: string - name: destinationId in: query required: true description: The ID of the parent folder, collection, or user in the Girder data hierarchy under which to import the files. schema: type: string - name: destinationType in: query required: false description: The type of the parent object to import into. schema: type: string enum: - folder - user - collection default: folder - name: limit in: query required: false description: The maximum number of studies to import. schema: type: string - name: filters in: query required: false description: Any search parameters to filter the studies query. schema: type: string default: '{}' - name: progress in: query required: false description: Whether to record progress on this operation. schema: type: boolean default: false responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not an administrator. summary: Import references to DICOM objects from a DICOMweb server tags: - dicomweb_assetstore /file: post: description: Use POST /file/chunk to send the contents of the file. The data for the first chunk of the file can be included with this query by sending it as the body of the request using an appropriate content-type and with the other parameters as part of the query string. If the entire file is uploaded via this call, the resulting file is returned. operationId: file_initUpload_post_file parameters: - name: parentType in: query required: true description: Type being uploaded into. schema: type: string enum: - folder - item - name: parentId in: query required: true description: The ID of the parent. schema: type: string - name: name in: query required: true description: Name of the file being created. schema: type: string - name: size in: query required: false description: Size in bytes of the file. schema: type: integer format: int32 - name: mimeType in: query required: false description: The MIME type of the file. schema: type: string - name: linkUrl in: query required: false description: If this is a link file, pass its URL instead of size and mimeType using this parameter. schema: type: string - name: reference in: query required: false description: If included, this information is passed to the data.process event when the upload is complete. schema: type: string - name: assetstoreId in: query required: false description: Direct the upload to a specific assetstore (admin-only). schema: type: string - name: uploadExtraParameters in: query required: false description: Arbitrary data to send along with the upload request. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Upload' '400': description: A parameter was invalid. '403': description: Write access was denied on the parent folder. '500': description: Failed to create upload. summary: Start a new upload or create an empty or link file. tags: - file /file/chunk: post: description: The data for the chunk should be sent as the body of the request using an appropriate content-type and with the other parameters as part of the query string. operationId: file_readChunk_post_chunk parameters: - name: offset in: query required: false description: Offset of the chunk in the file. schema: type: integer format: int32 default: 0 - name: uploadExtraParameters in: query required: false description: Arbitrary data to send along with the upload request. schema: type: string responses: '200': description: Success '400': description: 'ID was invalid. Received too many bytes. Chunk is smaller than the minimum size.' '403': description: You are not the user who initiated the upload. '500': description: Failed to store upload. summary: Upload a chunk of a file. tags: - file requestBody: content: multipart/form-data: schema: type: object properties: uploadId: type: string description: The ID of the document. required: - uploadId /file/completion: post: description: This is only required in certain non-standard upload behaviors. Clients should know which behavior models require the finalize step to be called in their behavior handlers. operationId: file_finalizeUpload_post_completion parameters: [] responses: '200': description: Success '400': description: 'ID was invalid. The upload does not require finalization. Not enough bytes have been uploaded.' '403': description: You are not the user who initiated the upload. summary: Finalize an upload explicitly if necessary. tags: - file requestBody: content: multipart/form-data: schema: type: object properties: uploadId: type: string description: The ID of the document. required: - uploadId /file/hashsum/{algo}/{hash}: get: operationId: file_getByHash_hashsum_algo_hash parameters: - name: algo in: path required: true description: The type of the given hashsum (case insensitive). schema: type: string enum: - sha512 - name: hash in: path required: true description: The hexadecimal hashsum of the file to download (case insensitive). schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Return a list of files matching a hashsum. tags: - file /file/hashsum/{algo}/{hash}/download: get: operationId: file_downloadWithHash_hashsum_algo_hash_download parameters: - name: algo in: path required: true description: The type of the given hashsum (case insensitive). schema: type: string enum: - sha512 - name: hash in: path required: true description: The hexadecimal hashsum of the file to download (case insensitive). schema: type: string responses: '200': description: Success '400': description: No file with the given hash exists. summary: Download a file by its hashsum. tags: - file /file/offset: get: operationId: file_requestOffset_offset parameters: [] responses: '200': description: Success '400': description: The ID was invalid, or the offset did not match the server's record. summary: Request required offset before resuming an upload. tags: - file requestBody: content: multipart/form-data: schema: type: object properties: uploadId: type: string description: The ID of the document. required: - uploadId /file/query: get: operationId: file_getFilesByQuery_query parameters: - name: query in: query required: true description: Find files that match this Mongo query. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _id - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/File' type: array '400': description: A parameter was invalid. summary: List files that match a query. tags: - file /file/upload/{id}: delete: operationId: file_cancelUpload_delete_upload_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: You lack permission to cancel this upload. summary: Cancel a partially completed upload. tags: - file /file/{id}: delete: operationId: file_deleteFile_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied on the parent folder. summary: Delete a file by ID. tags: - file get: operationId: file_getFile_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the file. summary: Get a file's information. tags: - file put: operationId: file_updateFile_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: query required: false description: The name to set on the file. schema: type: string - name: mimeType in: query required: false description: The MIME type of the file. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied on the parent folder. summary: Change file metadata such as name or MIME type. tags: - file /file/{id}/contents: put: description: After calling this, send the chunks just like you would with a normal file upload. operationId: file_updateFileContents_put_id_contents parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: size in: query required: true description: Size in bytes of the new file. schema: type: integer format: int32 - name: reference in: query required: false description: If included, this information is passed to the data.process event when the upload is complete. schema: type: string - name: assetstoreId in: query required: false description: Direct the upload to a specific assetstore (admin-only). schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Change the contents of an existing file. tags: - file /file/{id}/copy: post: operationId: file_copy_post_id_copy parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Copy a file. tags: - file requestBody: content: multipart/form-data: schema: type: object properties: itemId: type: string description: The ID of the item to copy the file to. required: - itemId /file/{id}/download: get: description: This endpoint also accepts the HTTP "Range" header for partial file downloads. operationId: file_download_id_download parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: offset in: query required: false description: Start downloading at this offset in bytes within the file. schema: type: integer format: int32 default: 0 - name: endByte in: query required: false description: If you only wish to download part of the file, pass this as the index of the last byte to download. Unlike the HTTP Range header, the endByte parameter is non-inclusive, so you should set it to the index of the byte one past the final byte you wish to receive. schema: type: integer format: int32 - name: contentDisposition in: query required: false description: Specify the Content-Disposition response header disposition-type value. schema: type: string enum: - inline - attachment default: attachment - name: extraParameters in: query required: false description: Arbitrary data to send along with the download request. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied on the parent folder. summary: Download a file. tags: - file /file/{id}/download/{name}: get: description: The name parameter doesn't alter the download. Some download clients save files based on the last part of a path, and specifying the name satisfies those clients. operationId: file_downloadWithName_id_download_name parameters: - name: id in: path required: true description: The ID of the file. schema: type: string - name: name in: path required: true description: The name of the file. This is ignored. schema: type: string - name: offset in: query required: false description: Start downloading at this offset in bytes within the file. schema: type: integer format: int32 responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied on the parent folder. summary: Download a file. tags: - file /file/{id}/hashsum: post: operationId: file_computeHashes_post_id_hashsum parameters: - name: id in: path required: true description: The ID of the file. schema: type: string - name: progress in: query required: false description: Whether to track progress of the operation schema: type: boolean default: false responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Write access was denied on the file. summary: Manually compute the checksum values for a given file. tags: - file /file/{id}/hashsum_file/{algo}: get: description: This is meant to be used in conjunction with CMake's ExternalData module. operationId: file_downloadKeyFile_id_hashsum_file_algo parameters: - name: id in: path required: true description: The ID of the file. schema: type: string - name: algo in: path required: true description: The hashsum algorithm. schema: type: string enum: - sha512 responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the file. summary: Download the hashsum key file for a given file. tags: - file /file/{id}/import/adjust_path: post: operationId: file_adjustFileImportPath_post_id_import_adjust_path parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: path in: query required: true description: The new import path of the file. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/File' '400': description: ID was invalid. '403': description: Write access was denied on the parent folder. summary: Adjust the import path of a file. tags: - file /file/{id}/move: put: operationId: file_moveFileToAssetstore_put_id_move parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: progress in: query required: false description: Controls whether progress notifications will be sent. schema: type: boolean default: false responses: '200': description: Success '400': description: A parameter was invalid. summary: Move a file to a different assetstore. tags: - file requestBody: content: multipart/form-data: schema: type: object properties: assetstoreId: type: string description: The destination assetstore. required: - assetstoreId /files: get: operationId: files_filesResponseRoot_files responses: '200': description: Success '400': description: A parameter was invalid. summary: List subitems or download a resource based on its path tags: - files parameters: [] /files/{path}: get: operationId: files_filesResponse_path parameters: - name: path in: path required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: List subitems or download a resource based on its path tags: - files /folder: get: description: 'You must pass either a "folderId" or "text" field to specify how you are searching for folders. If you omit one of these parameters the request will fail and respond : "Invalid search mode."' operationId: folder_find_folder parameters: - name: parentType in: query required: false description: Type of the folder's parent schema: type: string enum: - folder - user - collection - name: parentId in: query required: false description: The ID of the folder's parent. schema: type: string - name: text in: query required: false description: Pass to perform a text search. schema: type: string - name: name in: query required: false description: Pass to lookup a folder by exact name match. Must pass parentType and parentId as well when using this. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lowerName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/Folder' type: array '400': description: A parameter was invalid. '403': description: Read access was denied on the parent resource. summary: Search for folders by certain properties. tags: - folder post: operationId: folder_createFolder_post_folder parameters: - name: parentType in: query required: false description: Type of the folder's parent schema: type: string enum: - folder - user - collection default: folder - name: parentId in: query required: true description: The ID of the folder's parent. schema: type: string - name: name in: query required: true description: Name of the folder. schema: type: string - name: description in: query required: false description: Description for the folder. schema: type: string default: '' - name: reuseExisting in: query required: false description: Return existing folder if it exists rather than creating a new one. schema: type: boolean default: false - name: public in: query required: false description: Whether the folder should be publicly visible. By default, inherits the value from parent folder, or in the case of user or collection parentType, defaults to False. schema: type: boolean - name: isVirtual in: query required: false description: Whether this is a virtual folder. schema: type: boolean - name: virtualItemsQuery in: query required: false description: Query to use to do virtual item lookup, as JSON. schema: type: string - name: virtualItemsSort in: query required: false description: Sort to use during virtual item lookup, as JSON. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: A parameter was invalid. '403': description: Write access was denied on the parent summary: Create a new folder. tags: - folder requestBody: content: multipart/form-data: schema: type: object properties: metadata: type: string description: A JSON object containing the metadata keys to add /folder/query: get: operationId: folder_getFoldersByQuery_query parameters: - name: query in: query required: true description: Find folders that match this Mongo query. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _id - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/Folder' type: array '400': description: A parameter was invalid. summary: List folders that match a query. tags: - folder /folder/{id}: delete: operationId: folder_deleteFolder_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin access was denied for the folder. summary: Delete a folder by ID. tags: - folder get: operationId: folder_getFolder_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: ID was invalid. '403': description: Read access was denied for the folder. summary: Get a folder by ID. tags: - folder put: operationId: folder_updateFolder_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: query required: false description: Name of the folder. schema: type: string - name: description in: query required: false description: Description for the folder. schema: type: string - name: parentType in: query required: false description: Type of the folder's parent schema: type: string enum: - folder - user - collection - name: parentId in: query required: false description: Parent ID for the new parent of this folder. schema: type: string - name: isVirtual in: query required: false description: Whether this is a virtual folder. schema: type: boolean - name: virtualItemsQuery in: query required: false description: Query to use to do virtual item lookup, as JSON. schema: type: string - name: virtualItemsSort in: query required: false description: Sort to use during virtual item lookup, as JSON. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: ID was invalid. '403': description: Write access was denied for the folder or its new parent object. summary: Update a folder or move it into a new parent. tags: - folder requestBody: content: multipart/form-data: schema: type: object properties: metadata: type: string description: A JSON object containing the metadata keys to add /folder/{id}/access: get: operationId: folder_getFolderAccess_id_access parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: ID was invalid. '403': description: Admin access was denied for the folder. summary: Get the access control list for a folder. tags: - folder put: operationId: folder_updateFolderAccess_put_id_access parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: access in: query required: true description: The JSON-encoded access control list. schema: type: string - name: publicFlags in: query required: false description: JSON list of public access flags. schema: type: string - name: public in: query required: false description: Whether the folder should be publicly visible. schema: type: boolean - name: recurse in: query required: false description: Whether the policies should be applied to all subfolders under this folder as well. schema: type: boolean default: false - name: progress in: query required: false description: If recurse is set to True, this controls whether progress notifications will be sent. schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin access was denied for the folder. summary: Update the access control list for a folder. tags: - folder /folder/{id}/contents: delete: description: Cleans out all the items and subfolders from under a folder, but does not remove the folder itself. operationId: folder_deleteContents_delete_id_contents parameters: - name: id in: path required: true description: The ID of the folder to clean. schema: type: string - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied on the folder. summary: Remove all contents from a folder. tags: - folder /folder/{id}/copy: post: operationId: folder_copyFolder_post_id_copy parameters: - name: id in: path required: true description: The ID of the original folder. schema: type: string - name: parentType in: query required: false description: Type of the new folder's parent schema: type: string enum: - folder - user - collection - name: parentId in: query required: false description: The ID of the parent document. schema: type: string - name: name in: query required: false description: Name for the new folder. schema: type: string - name: description in: query required: false description: Description for the new folder. schema: type: string - name: public in: query required: false description: Whether the folder should be publicly visible. By default, inherits the value from parent folder, or in the case of user or collection parentType, defaults to False. If 'original', use the value of the original folder. schema: type: string enum: - 'true' - 'false' - original - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false - name: copyAnnotations in: query required: false description: Copy annotations when copying folder (default true) schema: type: boolean responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: 'A parameter was invalid. ID was invalid.' '403': description: 'Read access was denied on the original folder. Write access was denied on the parent.' summary: Copy a folder. tags: - folder /folder/{id}/details: get: operationId: folder_getFolderDetails_id_details parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the folder. summary: Get detailed information about a folder. tags: - folder /folder/{id}/download: get: operationId: folder_downloadFolder_id_download parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: mimeFilter in: query required: false description: JSON list of MIME types to include. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the folder. summary: Download an entire folder as a zip archive. tags: - folder /folder/{id}/metadata: delete: operationId: folder_deleteMetadata_delete_id_metadata parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the folder. summary: Delete metadata fields on a folder. tags: - folder requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON list containing the metadata fields to delete put: description: Set metadata fields to null in order to delete them. operationId: folder_setMetadata_put_id_metadata parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: allowNull in: query required: false description: Whether "null" is allowed as a metadata value. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Folder' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the folder. summary: Set metadata fields on an folder. tags: - folder requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata keys to add /folder/{id}/move: put: operationId: folder_moveFolder_put_id_move parameters: - name: id in: path required: true description: Source folder ID schema: type: string - name: ignoreImported in: query required: true description: Ignore files that have been directly imported schema: type: boolean default: true - name: progress in: query required: false description: Whether to record progress on the move. schema: type: boolean default: false responses: '200': description: Success '400': description: A parameter was invalid. summary: Move folder contents to an assetstore. tags: - folder requestBody: content: multipart/form-data: schema: type: object properties: assetstoreId: type: string description: Destination assetstore ID required: - assetstoreId /folder/{id}/position: get: description: 'You must pass either a "folderId" or "text" field to specify how you are searching for folders. If you omit one of these parameters the request will fail and respond : "Invalid search mode."' operationId: folder_findPosition_id_position parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: parentType in: query required: false description: Type of the folder's parent schema: type: string enum: - folder - user - collection - name: parentId in: query required: false description: The ID of the folder's parent. schema: type: string - name: text in: query required: false description: Pass to perform a text search. schema: type: string - name: name in: query required: false description: Pass to lookup a folder by exact name match. Must pass parentType and parentId as well when using this. schema: type: string - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lowerName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the parent resource. summary: Report the offset of a folder in a list or search. tags: - folder /folder/{id}/rootpath: get: operationId: folder_rootpath_id_rootpath parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the folder. summary: Get the path to the root of the folder's hierarchy. tags: - folder /folder/{id}/yaml_config/{name}: get: description: 'This walks up the chain of parent folders until the file is found. If not found, the .config folder in the parent collection or user is checked. Any yaml file can be returned. If the top-level is a dictionary and contains keys "access" or "groups" where those are dictionaries, the returned value will be modified based on the current user. The "groups" dictionary contains keys that are group names and values that update the main dictionary. All groups that the user is a member of are merged in alphabetical order. If a key and value of "\__all\__": True exists, the replacement is total; otherwise it is a merge. If the "access" dictionary exists, the "user" and "admin" subdictionaries are merged if a calling user is present and if the user is an admin, respectively (both get merged for admins).' operationId: folder_getYAMLConfigFile_id_yaml_config_name parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: path required: true description: The name of the file. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a config file. tags: - folder put: description: This replaces or creates an item in the specified folder with the specified name containing a single file also of the specified name. The file is added to the default assetstore, and any existing file may be permanently deleted. operationId: folder_putYAMLConfigFile_put_id_yaml_config_name parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: path required: true description: The name of the file. schema: type: string - name: user_context in: query required: true description: Whether these settings should only apply to the current user. schema: type: boolean default: false responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a config file. tags: - folder requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: The contents of yaml config file to validate. /group: get: operationId: group_find_group parameters: - name: text in: query required: false description: Pass this to perform a full-text search for groups. schema: type: string - name: exact in: query required: false description: If true, only return exact name matches. This is case sensitive. schema: type: boolean default: false - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Search for groups or list all groups. tags: - group post: description: Must be logged in. operationId: group_createGroup_post_group parameters: - name: name in: query required: true description: Unique name for the group. schema: type: string - name: description in: query required: false description: Description of the group. schema: type: string default: '' - name: public in: query required: false description: Whether the group should be publicly visible. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: A parameter was invalid. '403': description: Write access was denied on the parent summary: Create a new group. tags: - group /group/{id}: delete: operationId: group_deleteGroup_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin access was denied for the group. summary: Delete a group by ID. tags: - group get: operationId: group_getGroup_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: ID was invalid. '403': description: Read access was denied for the group. summary: Get a group by ID. tags: - group put: operationId: group_updateGroup_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: query required: false description: The name to set on the group. schema: type: string - name: description in: query required: false description: Description for the group. schema: type: string - name: public in: query required: false description: Whether the group should be publicly visible schema: type: boolean - name: addAllowed in: query required: false description: Can admins or moderators directly add members to this group? Only system administrators are allowed to set this field schema: type: string enum: - default - 'no' - yesmod - yesadmin responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Write access was denied for the group. summary: Update a group by ID. tags: - group /group/{id}/access: get: operationId: group_getGroupAccess_id_access parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: ID was invalid. '403': description: Read access was denied for the group. summary: Get the access control list for a group. tags: - group /group/{id}/admin: delete: operationId: group_demote_delete_id_admin parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: A parameter was invalid. '403': description: You don't have permission to demote users. summary: Demote a user to a normal group member. tags: - group requestBody: content: multipart/form-data: schema: type: object properties: userId: type: string description: The ID of the user to demote. required: - userId post: operationId: group_promoteToAdmin_post_id_admin parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: ID was invalid. '403': description: You don't have permission to promote users. summary: Promote a member to be an administrator of the group. tags: - group requestBody: content: multipart/form-data: schema: type: object properties: userId: type: string description: The ID of the user to promote. required: - userId /group/{id}/invitation: get: operationId: group_getGroupInvitations_id_invitation parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lastName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: A parameter was invalid. '403': description: Read access was denied for the group. summary: Show outstanding invitations for a group. tags: - group post: description: The "force" option to this endpoint is only available to administrators and can be used to bypass the invitation process and instead add the user directly to the group. operationId: group_inviteToGroup_post_id_invitation parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: level in: query required: false description: The access level the user will be given when they accept the invitation. schema: type: integer format: int32 default: 0 - name: quiet in: query required: false description: If you do not want this action to send an email to the target user, set this to true. schema: type: boolean default: false - name: force in: query required: false description: Add user directly rather than sending an invitation (admin-only option). schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: A parameter was invalid. '403': description: Write access was denied for the group. summary: Invite a user to join a group, or accept a user's request to join. tags: - group requestBody: content: multipart/form-data: schema: type: object properties: userId: type: string description: The ID of the user to invite or accept. required: - userId /group/{id}/member: delete: description: If the specified user is not yet a member of the group, this will delete any outstanding invitation or membership request for the user. Passing no userId parameter will assume that the current user is removing themself. operationId: group_removeFromGroup_delete_id_member parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: A parameter was invalid. '403': description: You don't have permission to remove that user. summary: Remove a user from a group, or uninvite them. tags: - group requestBody: content: multipart/form-data: schema: type: object properties: userId: type: string description: The ID of the user to remove. If not passed, will remove yourself from the group. get: operationId: group_listMembers_id_member parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lastName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the group. summary: List members of a group. tags: - group post: operationId: group_joinGroup_post_id_member parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: ID was invalid. '403': description: You were not invited to this group, or do not have read access to it. summary: Request to join a group, or accept an invitation to join. tags: - group /group/{id}/moderator: delete: operationId: group_demote_delete_id_moderator parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: A parameter was invalid. '403': description: You don't have permission to demote users. summary: Demote a user to a normal group member. tags: - group requestBody: content: multipart/form-data: schema: type: object properties: userId: type: string description: The ID of the user to demote. required: - userId post: operationId: group_promoteToModerator_post_id_moderator parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Group' '400': description: ID was invalid. '403': description: You don't have permission to promote users. summary: Promote a member to be a moderator of the group. tags: - group requestBody: content: multipart/form-data: schema: type: object properties: userId: type: string description: The ID of the user to promote. required: - userId /histomicsui/child_metadata/{id}: get: operationId: histomicsui_getChildMetadata_child_metadata_id parameters: - name: id in: path required: true description: The ID of the resource. schema: type: string - name: type in: query required: true description: The type of the resource schema: type: string enum: - folder - collection - user responses: '200': description: Success '400': description: ID was invalid. '403': description: Access was denied for the resource. summary: Get all metadata for a resource and all folders and items that are children of a resource. tags: - histomicsui /histomicsui/quarantine/{id}: put: operationId: histomicsui_putQuarantine_put_quarantine_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: ID was invalid. '403': description: Write access was denied for the item summary: Move an item to the quarantine folder. tags: - histomicsui /histomicsui/quarantine/{id}/restore: put: operationId: histomicsui_restoreQuarantine_put_quarantine_id_restore parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: ID was invalid. '403': description: Write access was denied for the item summary: Restore a quarantined item to its original folder. tags: - histomicsui /histomicsui/query_metadata: get: operationId: histomicsui_findItemsByMetadata_query_metadata parameters: - name: key in: query required: true description: The metadata key schema: type: string - name: value in: query required: true description: The (json encoded) metadata value schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: 'Required parameters were not provided. Invalid value provided.' summary: Get a list of items with a specific metadata value. tags: - histomicsui /histomicsui/settings: get: operationId: histomicsui_getPublicSettings_settings responses: '200': description: Success '400': description: A parameter was invalid. summary: Get public settings for HistomicsUI. tags: - histomicsui parameters: [] /homepage: get: operationId: homepage_getSettings_homepage responses: '200': description: Success '400': description: A parameter was invalid. summary: Public url for getting the homepage properties. tags: - homepage parameters: [] /homepage/assets: get: operationId: homepage_getAssets_assets responses: '200': description: Success '400': description: A parameter was invalid. summary: Return the folder IDs for uploaded asset content. tags: - homepage parameters: [] /item: get: description: 'You must pass either a "folderId" or "text" field to specify how you are searching for items. If you omit one of these parameters the request will fail and respond : "Invalid search mode."' operationId: item_find_item parameters: - name: folderId in: query required: false description: Pass this to list all items in a folder. schema: type: string - name: text in: query required: false description: Pass this to perform a full text search for items. schema: type: string - name: name in: query required: false description: Pass to lookup an item by exact name match. Must pass folderId as well when using this. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lowerName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/Item' type: array '400': description: A parameter was invalid. '403': description: Read access was denied on the parent folder. summary: List or search for items. tags: - item post: operationId: item_createItem_post_item parameters: - name: folderId in: query required: true description: The ID of the parent folder. schema: type: string - name: name in: query required: true description: Name for the item. schema: type: string - name: description in: query required: false description: Description for the item. schema: type: string default: '' - name: reuseExisting in: query required: false description: Return existing item (by name) if it exists. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: A parameter was invalid. '403': description: Write access was denied on the parent folder. summary: Create a new item. tags: - item requestBody: content: multipart/form-data: schema: type: object properties: metadata: type: string description: A JSON object containing the metadata keys to add /item/query: get: operationId: item_getItemsByQuery_query parameters: - name: query in: query required: true description: Find items that match this Mongo query. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _id - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/Item' type: array '400': description: A parameter was invalid. summary: List items that match a query. tags: - item /item/test/tiles: get: operationId: item_getTestTilesInfo_test_tiles responses: '200': description: Success '400': description: A parameter was invalid. summary: Get test large image metadata. tags: - item parameters: [] /item/test/tiles/zxy/{z}/{x}/{y}: get: operationId: item_getTestTile_test_tiles_zxy_z_x_y parameters: - name: z in: path required: true description: The layer number of the tile (0 is the most zoomed-out layer). schema: type: string - name: x in: path required: true description: The X coordinate of the tile (0 is the left side). schema: type: string - name: y in: path required: true description: The Y coordinate of the tile (0 is the top). schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a test large image tile. tags: - item /item/{id}: delete: operationId: item_deleteItem_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the item. summary: Delete an item by ID. tags: - item get: operationId: item_getItem_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get an item by ID. tags: - item put: operationId: item_updateItem_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: name in: query required: false description: Name for the item. schema: type: string - name: description in: query required: false description: Description for the item. schema: type: string - name: folderId in: query required: false description: Pass this to move the item to a new folder. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: ID was invalid. '403': description: Write access was denied for the item or folder. summary: Edit an item or move it to another folder. tags: - item requestBody: content: multipart/form-data: schema: type: object properties: metadata: type: string description: A JSON object containing the metadata keys to add /item/{id}/adjacent_images: get: operationId: item_getPreviousAndNextImages_id_adjacent_images parameters: - name: id in: path required: true description: The current item ID schema: type: string - name: folderId in: query required: false description: The (virtual) folder ID the image is located in schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '404': description: Image not found summary: Get the previous and next image in the same folder as the given item. tags: - item /item/{id}/aperio: delete: operationId: item_removeAperio_delete_id_aperio parameters: - name: id in: path required: true description: The ID of the annotation item schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove Aperio specific metadata from an item tags: - item get: operationId: item_findAperio_id_aperio parameters: - name: id in: path required: true description: The ID of the slide image item schema: type: string - name: tag in: query required: false description: Filter by the given tag string schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Find Aperio annotation items associated with a slide image. tags: - item post: operationId: item_importDocument_post_id_aperio parameters: - name: id in: path required: true description: The ID of the item containing the annotation file schema: type: string - name: imageId in: query required: true description: The ID of the slide image schema: type: string - name: tag in: query required: false description: A searchable tag to store with the metadata schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Import an item as an Aperio annotation tags: - item put: operationId: item_modifyAperio_put_id_aperio parameters: - name: id in: path required: true description: The ID of the annotation file schema: type: string - name: tag in: query required: true description: A searchable tag to store with the metadata schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Set the tag associated with the annotation file tags: - item /item/{id}/copy: post: description: If no folderId parameter is specified, creates a copy of the item in its current containing folder. operationId: item_copyItem_post_id_copy parameters: - name: id in: path required: true description: The ID of the original item. schema: type: string - name: folderId in: query required: false description: The ID of the parent folder. schema: type: string - name: name in: query required: false description: Name for the new item. schema: type: string - name: description in: query required: false description: Description for the new item. schema: type: string - name: copyAnnotations in: query required: false description: Copy annotations when copying item (default true) schema: type: boolean responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: 'A parameter was invalid. ID was invalid.' '403': description: 'Read access was denied on the original item. Write access was denied on the parent folder.' summary: Copy an item. tags: - item /item/{id}/download: get: operationId: item_download_id_download parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: offset in: query required: false description: Byte offset into the file. schema: type: integer format: int32 default: 0 - name: format in: query required: false description: If unspecified, items with one file are downloaded as that file, and other items are downloaded as a zip archive. If 'zip', a zip archive is always sent. schema: type: string - name: contentDisposition in: query required: false description: Specify the Content-Disposition response header disposition-type value, only applied for single file items. schema: type: string enum: - inline - attachment default: attachment - name: extraParameters in: query required: false description: Arbitrary data to send along with the download request, only applied for single file items. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Download the contents of an item. tags: - item /item/{id}/files: get: operationId: item_getFiles_id_files parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/File' type: array '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get the files within an item. tags: - item /item/{id}/metadata: delete: operationId: item_deleteMetadata_delete_id_metadata parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the item. summary: Delete metadata fields on an item. tags: - item requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON list containing the metadata fields to delete put: description: Set metadata fields to null in order to delete them. operationId: item_setMetadata_put_id_metadata parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: allowNull in: query required: false description: Whether "null" is allowed as a metadata value. schema: type: boolean default: false responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Item' '400': description: 'ID was invalid. Invalid JSON passed in request body. Metadata key name was invalid.' '403': description: Write access was denied for the item. summary: Set metadata fields on an item. tags: - item requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata keys to add /item/{id}/next_image: get: operationId: item_getNextImage_id_next_image parameters: - name: id in: path required: true description: The current image ID schema: type: string - name: folderId in: query required: false description: The (virtual) folder ID the image is located in schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '404': description: Image not found summary: Get the next image in the same folder as the given item. tags: - item /item/{id}/position: get: description: 'You must pass either a "folderId" or "text" field to specify how you are searching for items. If you omit one of these parameters the request will fail and respond : "Invalid search mode."' operationId: item_findPosition_id_position parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: folderId in: query required: false description: Pass this to list all items in a folder. schema: type: string - name: text in: query required: false description: Pass this to perform a full text search for items. schema: type: string - name: name in: query required: false description: Pass to lookup an item by exact name match. Must pass folderId as well when using this. schema: type: string - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lowerName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the parent folder. summary: Report the offset of an item in a list or search. tags: - item /item/{id}/previous_image: get: operationId: item_getPreviousImage_id_previous_image parameters: - name: id in: path required: true description: The current item ID schema: type: string - name: folderId in: query required: false description: The (virtual) folder ID the image is located in schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '404': description: Image not found summary: Get the previous image in the same folder as the given item. tags: - item /item/{id}/rootpath: get: operationId: item_rootpath_id_rootpath parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get the path to the root of the item's hierarchy. tags: - item /item/{itemId}/internal_metadata/{key}: delete: operationId: item_deleteMetadataKey_delete_itemId_internal_metadata_key parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: key in: path required: true description: The metadata key to delete. schema: type: string default: meta responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the item. summary: Delete a single internal metadata key on this item. tags: - item get: operationId: item_getMetadataKey_itemId_internal_metadata_key parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: key in: path required: true description: The metadata key to retrieve. schema: type: string default: meta responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get the value for a single internal metadata key on this item. tags: - item put: operationId: item_updateMetadataKey_put_itemId_internal_metadata_key parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: key in: path required: true description: The metadata key which should have a new value. The default key, "meta" is equivalent to the external metadata. Editing the "meta" key is equivalent to using PUT /item/{id}/metadata. schema: type: string default: meta responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the item. summary: Overwrite the value for a single internal metadata key on this item. tags: - item requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: The new value that should be written for the chosen metadata key /item/{itemId}/tiles: delete: operationId: item_deleteTiles_delete_itemId_tiles parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove a large image from this item. tags: - item get: operationId: item_getTilesInfo_itemId_tiles parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get large image metadata. tags: - item post: operationId: item_createTiles_post_itemId_tiles parameters: - name: itemId in: path required: true description: The source item. schema: type: string - name: fileId in: query required: false description: The source file containing the image. Required if there is more than one file in the item. schema: type: string - name: force in: query required: false description: Always use a job to create the large image. schema: type: boolean default: false - name: notify in: query required: false description: If a job is required to create the large image, a nofication can be sent when it is complete. schema: type: boolean default: true - name: localJob in: query required: false description: If true, run as a local job; if false, run via the remote worker schema: type: boolean - name: tileSize in: query required: false description: Tile size schema: type: integer format: int32 default: 256 - name: compression in: query required: false description: Internal compression format schema: type: string enum: - none - jpeg - deflate - lzw - zstd - packbits - webp - jp2k - name: quality in: query required: false description: JPEG compression quality where 0 is small and 100 is highest quality schema: type: integer format: int32 default: 90 - name: level in: query required: false description: Compression level for deflate (zip) or zstd. schema: type: integer format: int32 - name: predictor in: query required: false description: Predictor for deflate (zip) or lzw. schema: type: string enum: - none - horizontal - float - 'yes' - name: psnr in: query required: false description: JP2K compression target peak-signal-to-noise-ratio where 0 is lossless and otherwise higher numbers are higher quality schema: type: integer format: int32 - name: cr in: query required: false description: JP2K target compression ratio where 1 is lossless schema: type: integer format: int32 - name: concurrent in: query required: false description: Suggested number of maximum concurrent processes to use during conversion. Values less than or equal to 0 use the number of logical cpus less that value. Default is -2. schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Create a large image for this item. tags: - item /item/{itemId}/tiles/bands: get: operationId: item_getBandInformation_itemId_tiles_bands parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: frame in: query required: false description: For multiframe images, the 0-based frame number. This is ignored on non-multiframe images. schema: type: integer format: int32 responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get band information for a large image item. tags: - item /item/{itemId}/tiles/convert: post: description: This can be used to make an item that is a different internal format than the original item. operationId: item_convertImage_post_itemId_tiles_convert parameters: - name: itemId in: path required: true description: The source item. schema: type: string - name: fileId in: query required: false description: The source file containing the image. Required if there is more than one file in the item. schema: type: string - name: folderId in: query required: false description: The destination folder. schema: type: string - name: name in: query required: false description: A new name for the output item. schema: type: string - name: localJob in: query required: false description: If true, run as a local job; if false, run via the remote worker schema: type: boolean - name: tileSize in: query required: false description: Tile size schema: type: integer format: int32 default: 256 - name: onlyFrame in: query required: false description: Only convert a specific 0-based frame of a multiframe file. If not specified, all frames are converted. schema: type: integer format: int32 - name: format in: query required: false description: File format schema: type: string enum: - tiff - aperio - name: compression in: query required: false description: Internal compression format schema: type: string enum: - none - jpeg - deflate - lzw - zstd - packbits - webp - jp2k - name: quality in: query required: false description: JPEG compression quality where 0 is small and 100 is highest quality schema: type: integer format: int32 default: 90 - name: level in: query required: false description: Compression level for deflate (zip) or zstd. schema: type: integer format: int32 - name: predictor in: query required: false description: Predictor for deflate (zip) or lzw. schema: type: string enum: - none - horizontal - float - 'yes' - name: psnr in: query required: false description: JP2K compression target peak-signal-to-noise-ratio where 0 is lossless and otherwise higher numbers are higher quality schema: type: integer format: int32 - name: cr in: query required: false description: JP2K target compression ratio where 1 is lossless schema: type: integer format: int32 - name: concurrent in: query required: false description: Suggested number of maximum concurrent processes to use during conversion. Values less than or equal to 0 use the number of logical cpus less that value. Default is -2. schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Create a new large image item based on an existing item tags: - item /item/{itemId}/tiles/dzi.dzi: get: operationId: item_getDZIInfo_itemId_tiles_dzi.dzi parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: overlap in: query required: false description: Pixel overlap (default 0), must be non-negative. schema: type: integer format: int32 - name: tilesize in: query required: false description: Tile size (default 256), must be a power of 2 schema: type: integer format: int32 responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get DeepZoom compatible metadata. tags: - item /item/{itemId}/tiles/dzi_files/{level}/{xandy}: get: operationId: item_getDZITile_itemId_tiles_dzi_files_level_xandy parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: level in: path required: true description: The deepzoom layer number of the tile (8 is the most zoomed-out layer). schema: type: string - name: xandy in: path required: true description: The X and Y coordinate of the tile in the form (x)_(y).(extension) where (0_0 is the left top). schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a DeepZoom image tile. tags: - item /item/{itemId}/tiles/fzxy/{frame}/{z}/{x}/{y}: get: operationId: item_getTileWithFrame_itemId_tiles_fzxy_frame_z_x_y parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: frame in: path required: true description: The frame number of the tile. schema: type: string - name: z in: path required: true description: The layer number of the tile (0 is the most zoomed-out layer). schema: type: string - name: x in: path required: true description: The X coordinate of the tile (0 is the left side). schema: type: string - name: y in: path required: true description: The Y coordinate of the tile (0 is the top). schema: type: string - name: redirect in: query required: false description: If the tile exists as a complete file, allow an HTTP redirect instead of returning the data directly. The redirect might not have the correct mime type. "exact" must match the image encoding and quality parameters, "encoding" must match the image encoding but disregards quality, and "any" will redirect to any image if possible. schema: type: string enum: - 'false' - exact - encoding - any default: 'false' responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a large image tile with a frame number. tags: - item /item/{itemId}/tiles/histogram: get: description: This can take all of the parameters as the region endpoint, plus some histogram-specific parameters. Only typically used parameters are listed. The returned result is a list with one entry per channel (always one of L, LA, RGB, or RGBA colorspace). Each entry has the histogram values, bin edges, minimum and maximum values for the channel, and number of samples (pixels) used in the computation. operationId: item_getHistogram_itemId_tiles_histogram parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: width in: query required: false description: The maximum width of the analyzed region in pixels. schema: type: integer format: int32 default: 2048 - name: height in: query required: false description: The maximum height of the analyzed region in pixels. schema: type: integer format: int32 default: 2048 - name: resample in: query required: false description: If false, an existing level of the image is used for the histogram. If true, the internal values are interpolated to match the specified size as needed. 0-3 for a specific interpolation method (0-nearest, 1-lanczos, 2-bilinear, 3-bicubic) schema: type: string enum: - 'false' - 'true' - '0' - '1' - '2' - '3' default: 'false' - name: frame in: query required: false description: For multiframe images, the 0-based frame number. This is ignored on non-multiframe images. schema: type: integer format: int32 - name: bins in: query required: false description: The number of bins in the histogram. schema: type: integer format: int32 default: 256 - name: rangeMin in: query required: false description: The minimum value in the histogram. Defaults to the minimum value in the image. schema: type: number format: float - name: rangeMax in: query required: false description: The maximum value in the histogram. Defaults to the maximum value in the image. schema: type: number format: float - name: roundRange in: query required: false description: If true and neither a minimum or maximum is specified for the range, round the bin edges and adjust the number of bins for integer data with smaller ranges. schema: type: boolean default: false - name: density in: query required: false description: If true, scale the results by the number of samples. schema: type: boolean default: false - name: cache in: query required: false description: Report on or request caching the specified histogram for all frames. Scheduling creates a local job. schema: type: string enum: - none - report - schedule responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a histogram for any region of a large image item. tags: - item /item/{itemId}/tiles/images: get: operationId: item_getAssociatedImagesList_itemId_tiles_images parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a list of additional images associated with a large image. tags: - item /item/{itemId}/tiles/images/{image}: get: description: Because associated images may contain PHI, admin access to the item is required. operationId: item_getAssociatedImage_itemId_tiles_images_image parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: image in: path required: true description: The key of the associated image. schema: type: string - name: width in: query required: false description: The maximum width of the image in pixels. schema: type: integer format: int32 - name: height in: query required: false description: The maximum height of the image in pixels. schema: type: integer format: int32 - name: encoding in: query required: false description: Image output encoding schema: type: string enum: - JPEG - PNG - TIFF default: JPEG - name: contentDisposition in: query required: false description: Specify the Content-Disposition response header disposition-type value. schema: type: string enum: - inline - attachment - name: contentDispositionFilename in: query required: false description: Specify the filename used in the Content-Disposition response header. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get an image associated with a large image. tags: - item /item/{itemId}/tiles/images/{image}/metadata: get: operationId: item_getAssociatedImageMetadata_itemId_tiles_images_image_metadata parameters: - name: itemId in: path required: true description: The ID of the document. schema: type: string - name: image in: path required: true description: The key of the associated image. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get metadata for an image associated with a large image. tags: - item /item/{itemId}/tiles/internal_metadata: get: operationId: item_getInternalMetadata_itemId_tiles_internal_metadata parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get large image internal metadata. tags: - item /item/{itemId}/tiles/pixel: get: description: When frameList is provided, returns a list of pixel dictionaries, one for each frame. Otherwise returns a single pixel dictionary. operationId: item_getTilesPixel_itemId_tiles_pixel parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: left in: query required: false description: The left column (0-based) of the pixel. schema: type: number format: float - name: top in: query required: false description: The top row (0-based) of the pixel. schema: type: number format: float - name: units in: query required: false description: Units used for left and top. base_pixels are pixels at the maximum resolution, pixels and mm are at the specified magnfication, fraction is a scale of [0-1]. schema: type: string enum: - base_pixels - fraction - km - m - mag_pixels - mm - nm - proj4:EPSG:4326 - projection - um default: base_pixels - name: frame in: query required: false description: For multiframe images, the 0-based frame number. This is ignored on non-multiframe images. schema: type: integer format: int32 - name: frameList in: query required: false description: Comma-separated list of frame numbers to query. If provided, returns a list of pixel values for each frame. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a single pixel of a large image item. tags: - item /item/{itemId}/tiles/region: get: description: If neither width nor height is specified, the full resolution region is returned. If a width or height is specified, aspect ratio is always preserved (if both are given, the resulting image may be smaller in one of the two dimensions). When scaling must be applied, the image is downsampled from a higher resolution layer, never upsampled. operationId: item_getTilesRegion_itemId_tiles_region parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: left in: query required: false description: The left column (0-based) of the region to process. Negative values are offsets from the right edge. schema: type: number format: float - name: top in: query required: false description: The top row (0-based) of the region to process. Negative values are offsets from the bottom edge. schema: type: number format: float - name: right in: query required: false description: The right column (0-based from the left) of the region to process. The region will not include this column. Negative values are offsets from the right edge. schema: type: number format: float - name: bottom in: query required: false description: The bottom row (0-based from the top) of the region to process. The region will not include this row. Negative values are offsets from the bottom edge. schema: type: number format: float - name: regionWidth in: query required: false description: The width of the region to process. schema: type: number format: float - name: regionHeight in: query required: false description: The height of the region to process. schema: type: number format: float - name: units in: query required: false description: Units used for left, top, right, bottom, regionWidth, and regionHeight. base_pixels are pixels at the maximum resolution, pixels and mm are at the specified magnfication, fraction is a scale of [0-1]. schema: type: string enum: - base_pixels - fraction - km - m - mag_pixels - mm - nm - proj4:EPSG:4326 - projection - um default: base_pixels - name: width in: query required: false description: The maximum width of the output image in pixels. schema: type: integer format: int32 - name: height in: query required: false description: The maximum height of the output image in pixels. schema: type: integer format: int32 - name: fill in: query required: false description: A fill color. If output dimensions are specified and fill is specified and not "none", the output image is padded on either the sides or the top and bottom to the requested output size. Most css colors are accepted. schema: type: string - name: magnification in: query required: false description: Magnification of the output image. If neither width for height is specified, the magnification, mm_x, and mm_y parameters are used to select the output size. schema: type: number format: float - name: mm_x in: query required: false description: The size of the output pixels in millimeters schema: type: number format: float - name: mm_y in: query required: false description: The size of the output pixels in millimeters schema: type: number format: float - name: exact in: query required: false description: If magnification, mm_x, or mm_y are specified, they must match an existing level of the image exactly. schema: type: boolean default: false - name: frame in: query required: false description: For multiframe images, the 0-based frame number. This is ignored on non-multiframe images. schema: type: integer format: int32 - name: encoding in: query required: false description: Output image encoding. TILED generates a tiled tiff without the upper limit on image size the other options have. For geospatial sources, TILED will also have appropriate tagging. Pickle emits python pickle data with an optional specific protocol schema: type: string enum: - JPEG - PNG - TIFF - TILED - JFIF - AVIF - BMP - DIB - PCX - EPS - GIF - JPEG2000 - MPO - PPM - SGI - TGA - WEBP - XBM - pickle - pickle:3 - pickle:4 - pickle:5 default: JPEG - name: jpegQuality in: query required: false description: Quality used for generating JPEG images schema: type: integer format: int32 default: 95 - name: jpegSubsampling in: query required: false description: Chroma subsampling used for generating JPEG images. 0, 1, and 2 are full, half, and quarter resolution chroma respectively. schema: type: integer format: int32 enum: - '0' - '1' - '2' default: '0' - name: tiffCompression in: query required: false description: Compression method when storing a TIFF image schema: type: string enum: - none - raw - lzw - tiff_lzw - jpeg - deflate - tiff_adobe_deflate - name: style in: query required: false description: JSON-encoded style string schema: type: string - name: resample in: query required: false description: If false, an existing level of the image is used for the region. If true, the internal values are interpolated to match the specified size as needed. 0-3 for a specific interpolation method (0-nearest, 1-lanczos, 2-bilinear, 3-bicubic) schema: type: string enum: - 'false' - 'true' - '0' - '1' - '2' - '3' - name: contentDisposition in: query required: false description: Specify the Content-Disposition response header disposition-type value. schema: type: string enum: - inline - attachment - name: contentDispositionFilename in: query required: false description: Specify the filename used in the Content-Disposition response header. schema: type: string responses: '200': description: Success '400': description: 'ID was invalid. Insufficient memory.' '403': description: Read access was denied for the item. summary: Get any region of a large image item, optionally scaling it. tags: - item /item/{itemId}/tiles/thumbnail: get: description: Aspect ratio is always preserved. If both width and height are specified, the resulting thumbnail may be smaller in one of the two dimensions. If neither width nor height is given, a default size will be returned. This creates a thumbnail from the lowest level of the source image, which means that asking for a large thumbnail will not be a high-quality image. operationId: item_getTilesThumbnail_itemId_tiles_thumbnail parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: width in: query required: false description: The maximum width of the thumbnail in pixels. schema: type: integer format: int32 - name: height in: query required: false description: The maximum height of the thumbnail in pixels. schema: type: integer format: int32 - name: fill in: query required: false description: A fill color. If width and height are both specified and fill is specified and not "none", the output image is padded on either the sides or the top and bottom to the requested output size. Most css colors are accepted. schema: type: string - name: frame in: query required: false description: For multiframe images, the 0-based frame number. This is ignored on non-multiframe images. schema: type: integer format: int32 - name: encoding in: query required: false description: Output image encoding. TILED generates a tiled tiff without the upper limit on image size the other options have. For geospatial sources, TILED will also have appropriate tagging. Pickle emits python pickle data with an optional specific protocol schema: type: string enum: - JPEG - PNG - TIFF - TILED - JFIF - AVIF - BMP - DIB - PCX - EPS - GIF - JPEG2000 - MPO - PPM - SGI - TGA - WEBP - XBM - pickle - pickle:3 - pickle:4 - pickle:5 default: JPEG - name: contentDisposition in: query required: false description: Specify the Content-Disposition response header disposition-type value. schema: type: string enum: - inline - attachment - name: contentDispositionFilename in: query required: false description: Specify the filename used in the Content-Disposition response header. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a thumbnail of a large image item. tags: - item /item/{itemId}/tiles/thumbnails: delete: operationId: item_deleteTilesThumbnails_delete_itemId_tiles_thumbnails parameters: - name: itemId in: path required: true description: The ID of the document. schema: type: string - name: keep in: query required: false description: Number of thumbnails to keep. Ignored if a key is specified. schema: type: integer format: int32 default: 10000 - name: key in: query required: false description: A specific key to delete schema: type: string - name: thumbnail in: query required: false description: If a key is specified, true if the key is a thumbnail; false if the key is a data record schema: type: boolean responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Delete thumbnail and data files associated with a large_image item. tags: - item get: operationId: item_listTilesThumbnails_itemId_tiles_thumbnails parameters: - name: itemId in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: List all thumbnail and data files associated with a large_image item. tags: - item post: operationId: item_addTilesThumbnails_post_itemId_tiles_thumbnails parameters: - name: itemId in: path required: true description: The ID of the document. schema: type: string - name: key in: query required: true description: A specific key to delete schema: type: string - name: thumbnail in: query required: false description: If a key is specified, true if the key is a thumbnail; false if the key is a data record schema: type: boolean - name: mimeType in: query required: false description: The MIME type of the file. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/File' '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Associate or replace a thumbnail or data file with a large_image items. tags: - item requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: An image or data block to associated with the large_image item. /item/{itemId}/tiles/tile_frames: get: operationId: item_tileFrames_itemId_tiles_tile_frames parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: framesAcross in: query required: false description: How many frames across schema: type: integer format: int32 - name: frameList in: query required: false description: Comma-separated list of frames schema: type: string - name: cache in: query required: false description: Cache the results for future use schema: type: boolean default: false - name: left in: query required: false description: The left column (0-based) of the region to process. Negative values are offsets from the right edge. schema: type: number format: float - name: top in: query required: false description: The top row (0-based) of the region to process. Negative values are offsets from the bottom edge. schema: type: number format: float - name: right in: query required: false description: The right column (0-based from the left) of the region to process. The region will not include this column. Negative values are offsets from the right edge. schema: type: number format: float - name: bottom in: query required: false description: The bottom row (0-based from the top) of the region to process. The region will not include this row. Negative values are offsets from the bottom edge. schema: type: number format: float - name: regionWidth in: query required: false description: The width of the region to process. schema: type: number format: float - name: regionHeight in: query required: false description: The height of the region to process. schema: type: number format: float - name: units in: query required: false description: Units used for left, top, right, bottom, regionWidth, and regionHeight. base_pixels are pixels at the maximum resolution, pixels and mm are at the specified magnfication, fraction is a scale of [0-1]. schema: type: string enum: - base_pixels - fraction - km - m - mag_pixels - mm - nm - proj4:EPSG:4326 - projection - um default: base_pixels - name: width in: query required: false description: The maximum width of the output image in pixels. schema: type: integer format: int32 - name: height in: query required: false description: The maximum height of the output image in pixels. schema: type: integer format: int32 - name: fill in: query required: false description: A fill color. If output dimensions are specified and fill is specified and not "none", the output image is padded on either the sides or the top and bottom to the requested output size. Most css colors are accepted. schema: type: string - name: magnification in: query required: false description: Magnification of the output image. If neither width for height is specified, the magnification, mm_x, and mm_y parameters are used to select the output size. schema: type: number format: float - name: mm_x in: query required: false description: The size of the output pixels in millimeters schema: type: number format: float - name: mm_y in: query required: false description: The size of the output pixels in millimeters schema: type: number format: float - name: exact in: query required: false description: If magnification, mm_x, or mm_y are specified, they must match an existing level of the image exactly. schema: type: boolean default: false - name: frame in: query required: false description: For multiframe images, the 0-based frame number. This is ignored on non-multiframe images. schema: type: integer format: int32 - name: encoding in: query required: false description: Output image encoding. TILED generates a tiled tiff without the upper limit on image size the other options have. For geospatial sources, TILED will also have appropriate tagging. Pickle emits python pickle data with an optional specific protocol schema: type: string enum: - JPEG - PNG - TIFF - TILED - JFIF - AVIF - BMP - DIB - PCX - EPS - GIF - JPEG2000 - MPO - PPM - SGI - TGA - WEBP - XBM - pickle - pickle:3 - pickle:4 - pickle:5 default: JPEG - name: jpegQuality in: query required: false description: Quality used for generating JPEG images schema: type: integer format: int32 default: 95 - name: jpegSubsampling in: query required: false description: Chroma subsampling used for generating JPEG images. 0, 1, and 2 are full, half, and quarter resolution chroma respectively. schema: type: integer format: int32 enum: - '0' - '1' - '2' default: '0' - name: tiffCompression in: query required: false description: Compression method when storing a TIFF image schema: type: string enum: - none - raw - lzw - tiff_lzw - jpeg - deflate - tiff_adobe_deflate - name: style in: query required: false description: JSON-encoded style string schema: type: string - name: resample in: query required: false description: If false, an existing level of the image is used for the region. If true, the internal values are interpolated to match the specified size as needed. 0-3 for a specific interpolation method (0-nearest, 1-lanczos, 2-bilinear, 3-bicubic) schema: type: string enum: - 'false' - 'true' - '0' - '1' - '2' - '3' - name: contentDisposition in: query required: false description: Specify the Content-Disposition response header disposition-type value. schema: type: string enum: - inline - attachment - name: contentDispositionFilename in: query required: false description: Specify the filename used in the Content-Disposition response header. schema: type: string responses: '200': description: Success '400': description: 'ID was invalid. Insufficient memory.' '403': description: Read access was denied for the item. summary: Composite thumbnails of multiple frames into a single image. tags: - item /item/{itemId}/tiles/tile_frames/quad_info: get: operationId: item_tileFramesQuadInfo_itemId_tiles_tile_frames_quad_info parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: format in: query required: false description: Optional format parameters, such as "encoding=JPEG&jpegQuality=85&jpegSubsampling=1". If specified, these replace the defaults. schema: type: string - name: query in: query required: false description: Addition query parameters that would be passed to tile endpoints, such as style. schema: type: string - name: frameBase in: query required: false description: Starting frame number (default 0). If c/z/t/xy then step through values from 0 to number of that axis - 1. The axis specification in only useful for cache reporting or scheduling schema: type: integer format: int32 - name: frameStride in: query required: false description: Only use every frameStride frame of the image (default 1). c/z/t/xy to use the length of that axis schema: type: integer format: int32 - name: frameGroup in: query required: false description: Group frames when using multiple textures to keep boundaries at a multiple of the group size number. c/z/t/xy to use the length of that axis. schema: type: integer format: int32 - name: frameGroupFactor in: query required: false description: Ignore grouping if the resultant images would be more than this factor smaller than without grouping (default 4) schema: type: integer format: int32 - name: frameGroupStride in: query required: false description: Reorder frames based on the to stride (default 1). "auto" to use frameGroup / frameStride if that value is an integer. schema: type: integer format: int32 - name: maxTextureSize in: query required: false description: Maximum texture size in either dimension. This should be the smaller of a desired value and of the intended graphics environment texture buffer (default 16384). schema: type: integer format: int32 - name: maxTextures in: query required: false description: Maximum number of textures to use (default 1). schema: type: integer format: int32 - name: maxTotalTexturePixels in: query required: false description: Limit the total area of all combined textures (default 2**30). schema: type: integer format: int32 - name: alignment in: query required: false description: Individual frame alignment within a texture. Used to avoid jpeg artifacts from crossing frames (default 16). schema: type: integer format: int32 - name: maxFrameSize in: query required: false description: If specified, frames will never be larger than this, even if the texture size allows it (default None). schema: type: integer format: int32 - name: cache in: query required: false description: Report on or request caching the resultant frames. Scheduling creates a local job. schema: type: string enum: - none - report - schedule responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get parameters for using tile_frames as background sprite images. tags: - item /item/{itemId}/tiles/zxy/{z}/{x}/{y}: get: operationId: item_getTile_itemId_tiles_zxy_z_x_y parameters: - name: itemId in: path required: true description: The ID of the item. schema: type: string - name: z in: path required: true description: The layer number of the tile (0 is the most zoomed-out layer). schema: type: string - name: x in: path required: true description: The X coordinate of the tile (0 is the left side). schema: type: string - name: y in: path required: true description: The Y coordinate of the tile (0 is the top). schema: type: string - name: redirect in: query required: false description: If the tile exists as a complete file, allow an HTTP redirect instead of returning the data directly. The redirect might not have the correct mime type. "exact" must match the image encoding and quality parameters, "encoding" must match the image encoding but disregards quality, and "any" will redirect to any image if possible. schema: type: string enum: - 'false' - exact - encoding - any default: 'false' responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the item. summary: Get a large image tile. tags: - item /job: get: operationId: job_listJobs_job parameters: - name: userId in: query required: false description: The ID of the user whose jobs will be listed. If not passed or empty, will use the currently logged in user. If set to "None", will list all jobs that do not have an owning user. schema: type: string - name: parentId in: query required: false description: Id of the parent job. schema: type: string - name: types in: query required: false description: Filter for type schema: type: string - name: statuses in: query required: false description: Filter for status schema: type: string - name: handlers in: query required: false description: Filter for handler schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: created - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List jobs for a given user. tags: - job post: operationId: job_createJob_post_job parameters: - name: title in: query required: true description: Title of the job. schema: type: string - name: type in: query required: true description: Type of the job. schema: type: string - name: parentId in: query required: false description: ID of the parent job. schema: type: string - name: public in: query required: false description: Whether the job is publicly visible. schema: type: boolean default: false - name: handler in: query required: false description: Job handler string. schema: type: string - name: args in: query required: false description: Job arguments schema: type: string - name: kwargs in: query required: false description: Job keyword arguments schema: type: string - name: otherFields in: query required: false description: Other fields specific to the job handler schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Create a job model tags: - job /job/all: get: operationId: job_listAllJobs_all parameters: - name: types in: query required: false description: Filter for type schema: type: string - name: statuses in: query required: false description: Filter for status schema: type: string - name: handlers in: query required: false description: Filter for handler schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: created - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List all jobs. tags: - job /job/old: delete: operationId: job_deleteOldJobs_delete_old parameters: - name: age in: query required: false description: The minimum age in days. schema: type: integer format: int32 default: 1 - name: status in: query required: false description: A comma-separated list of statuses to include. Blank for all. schema: type: string default: 0,1,2 responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete old jobs. tags: - job get: operationId: job_getOldJobs_old parameters: - name: age in: query required: false description: The minimum age in days. schema: type: integer format: int32 default: 1 - name: status in: query required: false description: A comma-separated list of statuses to include. Blank for all. schema: type: string default: 0,1,2 responses: '200': description: Success '400': description: A parameter was invalid. summary: Report on old jobs. tags: - job /job/typeandstatus: get: operationId: job_jobsTypesAndStatuses_typeandstatus responses: '200': description: Success '400': description: A parameter was invalid. summary: Get types and statuses of jobs of current user tags: - job parameters: [] /job/typeandstatus/all: get: operationId: job_allJobsTypesAndStatuses_typeandstatus_all responses: '200': description: Success '403': description: Admin access was denied for the job. summary: Get types and statuses of all jobs tags: - job parameters: [] /job/{id}: delete: operationId: job_deleteJob_delete_id parameters: - name: id in: path required: true description: The ID of the job. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Admin access was denied for the job. summary: Delete an existing job. tags: - job get: operationId: job_getJob_id parameters: - name: id in: path required: true description: The ID of the job. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the job. summary: Get a job by ID. tags: - job put: description: In most cases, regular users should not call this endpoint. It will typically be used by a batch processing system to send updates regarding the execution of the job. If using a non-user-associated token for authorization, the token must be granted the "jobs.job_" scope, where is the ID of the job being updated. operationId: job_updateJob_put_id parameters: - name: id in: path required: true description: The ID of the job. schema: type: string - name: log in: query required: false description: A message to add to the job's log field. If you want to overwrite any existing log content, pass another parameter "overwrite=true". schema: type: string - name: overwrite in: query required: false description: If passing a log parameter, you may set this to "true" if you wish to overwrite the log field rather than append to it. schema: type: boolean default: false - name: status in: query required: false description: Update the status of the job. See the JobStatus enumeration in the constants module in this plugin for the numerical values of each status. schema: type: string - name: progressTotal in: query required: false description: Maximum progress value, set <= 0 to indicate indeterminate progress for this job. schema: type: number format: float - name: progressCurrent in: query required: false description: Current progress value. schema: type: number format: float - name: progressMessage in: query required: false description: Current progress message. schema: type: string - name: notify in: query required: false description: If this update should trigger a notification, set this field to true. schema: type: boolean default: true responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the job. summary: Update an existing job. tags: - job /job/{id}/cancel: put: operationId: job_cancelJob_put_id_cancel parameters: - name: id in: path required: true description: The ID of the job. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the job. summary: Cancel a job by ID. tags: - job /large_image/associated_images: delete: operationId: large_image_deleteAssociatedImages_delete_associated_images parameters: - name: imageKey in: query required: false description: If specific, only include images with the specified key schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete cached associated image files from large_image items. tags: - large_image get: description: The imageKey can also be "tileFrames". operationId: large_image_countAssociatedImages_associated_images parameters: - name: imageKey in: query required: false description: If specific, only include images with the specified key schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Count the number of cached associated image files for large_image items. tags: - large_image /large_image/cache: get: operationId: large_image_cacheInfo_cache responses: '200': description: Success '400': description: A parameter was invalid. summary: Get information on caches. tags: - large_image parameters: [] /large_image/cache/clear: put: operationId: large_image_cacheClear_put_cache_clear responses: '200': description: Success '400': description: A parameter was invalid. summary: Clear tile source caches to release resources and file handles. tags: - large_image parameters: [] /large_image/config/format: post: operationId: large_image_configFormat_post_config_format parameters: [] responses: '200': description: Success '400': description: A parameter was invalid. summary: Reformat a Girder config file tags: - large_image requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: The contents of config file to format. /large_image/config/replace: post: operationId: large_image_configReplace_post_config_replace parameters: - name: restart in: query required: false description: Whether to restart the server after updating the config file schema: type: boolean default: true responses: '200': description: Success '400': description: A parameter was invalid. summary: Replace the existing Girder config file tags: - large_image requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: The new contents of config file. /large_image/config/validate: post: description: Returns a list of errors found. operationId: large_image_configValidate_post_config_validate parameters: [] responses: '200': description: Success '400': description: A parameter was invalid. summary: Validate a Girder config file tags: - large_image requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: The contents of config file to validate. /large_image/folder/{id}/tiles: put: description: Does not work for new items with multiple files. operationId: large_image_createLargeImages_put_folder_id_tiles parameters: - name: id in: path required: true description: The ID of the folder. schema: type: string - name: createJobs in: query required: false description: If true, a job will be used to create the image when needed; if always, a job will always be used; if false, a job will never be used, creating a version of the image in a preferred format. schema: type: string enum: - 'true' - 'false' - always default: 'false' - name: localJobs in: query required: false description: If true, run each creation job locally; if false, run via the remote worker. schema: type: boolean default: 'false' - name: recurse in: query required: false description: If true, items in child folders will also be checked. schema: type: boolean default: false - name: cancelJobs in: query required: false description: If true, unfinished large image job(s) associated with items in the folder will be canceled, then a new large image created; if false, items with an unfinished large image will be skipped. schema: type: boolean default: false - name: redoExisting in: query required: false description: If true, existing large images should be removed and recreated. Otherwise they will be skipped. schema: type: boolean default: false responses: '200': description: Success '400': description: ID was invalid. '403': description: Write access was denied for the folder. summary: Create large images for all items within a folder. tags: - large_image /large_image/histograms: delete: operationId: large_image_deleteHistograms_delete_histograms responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete cached histograms from large_image items. tags: - large_image parameters: [] get: operationId: large_image_countHistograms_histograms responses: '200': description: Success '400': description: A parameter was invalid. summary: Count the number of cached histograms for large_image items. tags: - large_image parameters: [] /large_image/settings: get: operationId: large_image_getPublicSettings_settings responses: '200': description: Success '400': description: A parameter was invalid. summary: Get public settings for large image display. tags: - large_image parameters: [] /large_image/sources: get: operationId: large_image_listSources_sources responses: '200': description: Success '400': description: A parameter was invalid. summary: List all Girder tile sources with associated extensions, mime types, and versions. Lower values indicate a higher priority for an extension or mime type with that source. tags: - large_image parameters: [] /large_image/thumbnails: delete: operationId: large_image_deleteThumbnails_delete_thumbnails parameters: - name: spec in: query required: false description: A JSON list of thumbnail specifications to delete. If empty, all cached thumbnails are deleted. The specifications typically include width, height, encoding, and encoding options. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete cached thumbnail files from large_image items. tags: - large_image get: operationId: large_image_countThumbnails_thumbnails parameters: - name: spec in: query required: false description: A JSON list of thumbnail specifications to count. If empty, all cached thumbnails are counted. The specifications typically include width, height, encoding, and encoding options. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Count the number of cached thumbnail files for large_image items. tags: - large_image put: description: 'This creates a local job that processes all large_image items. A common spec for the Girder API is: [{"width": 160, "height": 100}, {"width": 160, "height": 100, "imageKey": "macro"}, {"width": 160, "height": 100, "imageKey": "label"}]' operationId: large_image_createThumbnails_put_thumbnails parameters: - name: spec in: query required: true description: A JSON list of thumbnail specifications to create. The specifications typically include width, height, encoding, and encoding options. schema: type: string - name: logInterval in: query required: false description: The number of seconds between log messages. This also determines how often the creation job is checked if it has been canceled or deleted. A value of 0 will log after each thumbnail is checked or created. schema: type: number format: float - name: concurrent in: query required: false description: The number of concurrent threads to use when making thumbnails. 0 or unspecified to base this on the number of reported cpus. schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Create cached thumbnail files from large_image items. tags: - large_image /large_image/tiles/incomplete: delete: description: This is used to clean up all large image conversion jobs that have failed to complete. If a job is in progress, it will be cancelled. The return value is the number of items that were adjusted. operationId: large_image_deleteIncompleteTiles_delete_tiles_incomplete responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove large images from items where the large image job incomplete. tags: - large_image parameters: [] /notification: get: description: This endpoint can be used for manual long-polling when SSE support is disabled or otherwise unavailable. The events are always returned in chronological order. operationId: notification_listNotifications_notification parameters: - name: since in: query required: false description: Filter out events before this date. schema: type: string format: date-time responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not logged in. summary: List notification events tags: - notification /notification/stream: get: description: This uses long-polling to keep the connection open for several minutes at a time (or longer) and should be requested with an EventSource object or other SSE-capable client.

Notifications are returned within a few seconds of when they occur. When no notification occurs for the timeout duration, the stream is closed.

This connection can stay open indefinitely long. operationId: notification_stream_stream parameters: - name: timeout in: query required: false description: The duration without a notification before the stream is closed. schema: type: integer format: int32 default: 300 - name: since in: query required: false description: Filter out events before this time stamp. schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. '403': description: You are not logged in. '503': description: The notification stream is not enabled. summary: Stream notifications for a given user via the SSE protocol. tags: - notification /resource: delete: operationId: resource_delete_delete_resource parameters: - name: resources in: query required: true description: 'A JSON-encoded set of resources to delete. Each type is a list of ids. For example: {"item": [(item id 1), (item id2)], "folder": [(folder id 1)]}.' schema: type: string - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false responses: '200': description: Success '400': description: 'Unsupported or unknown resource type. Invalid resources format. No resources specified. Resource not found.' '403': description: Admin access was denied for a resource. summary: Delete a set of items, folders, or other resources. tags: - resource /resource/copy: post: operationId: resource_copyResources_post_copy parameters: - name: resources in: query required: true description: 'A JSON-encoded set of resources to copy. Each type is a list of ids. Only folders and items may be specified. For example: {"item": [(item id 1), (item id2)], "folder": [(folder id 1)]}.' schema: type: string - name: parentType in: query required: true description: Parent type for the new parent of these resources. schema: type: string - name: parentId in: query required: true description: Parent ID for the new parent of these resources. schema: type: string - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false - name: copyAnnotations in: query required: false description: Copy annotations when copying resources (default true) schema: type: boolean responses: '200': description: Success '400': description: 'Unsupported or unknown resource type. Invalid resources format. Resource type not supported. No resources specified. Resource not found. ID was invalid.' summary: Copy a set of items and folders. tags: - resource /resource/download: get: description: This route is also exposed via the POST method because the request parameters can be quite long, and encoding them in the URL (as is standard when using the GET method) can cause the URL to become too long, which causes errors. operationId: resource_download_download parameters: - name: resources in: query required: true description: 'A JSON-encoded set of resources to download. Each type is a list of ids. For example: {"item": [(item id 1), (item id 2)], "folder": [(folder id 1)]}.' schema: type: string - name: includeMetadata in: query required: false description: Include any metadata in JSON files in the archive. schema: type: boolean default: false responses: '200': description: Success '400': description: 'Unsupported or unknown resource type. Invalid resources format. No resources specified. Resource not found.' '403': description: Read access was denied for a resource. summary: Download a set of items, folders, collections, and users as a zip archive. tags: - resource post: description: This route is also exposed via the POST method because the request parameters can be quite long, and encoding them in the URL (as is standard when using the GET method) can cause the URL to become too long, which causes errors. operationId: resource_download_post_download parameters: - name: resources in: query required: true description: 'A JSON-encoded set of resources to download. Each type is a list of ids. For example: {"item": [(item id 1), (item id 2)], "folder": [(folder id 1)]}.' schema: type: string - name: includeMetadata in: query required: false description: Include any metadata in JSON files in the archive. schema: type: boolean default: false responses: '200': description: Success '400': description: 'Unsupported or unknown resource type. Invalid resources format. No resources specified. Resource not found.' '403': description: Read access was denied for a resource. summary: Download a set of items, folders, collections, and users as a zip archive. tags: - resource /resource/lookup: get: operationId: resource_lookup_lookup parameters: - name: path in: query required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: Look up a resource in the data hierarchy by path. tags: - resource /resource/metadata: put: operationId: resource_putResourceMetadata_put_metadata parameters: - name: resources in: query required: true description: 'A JSON-encoded set of resources to modify. Each type is a list of ids. For example: {"item": [(item id 1), (item id 2)], "folder": [(folder id 1)]}.' schema: type: string - name: allowNull in: query required: false description: Whether "null" is allowed as a metadata value. schema: type: boolean default: false responses: '200': description: Success '400': description: 'Unsupported or unknown resource type. Invalid resources format. No resources specified. Resource not found.' '403': description: Write access was denied for a resource. summary: Set metadata on multiple resources at once. tags: - resource requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata keys to add /resource/move: put: operationId: resource_moveResources_put_move parameters: - name: resources in: query required: true description: 'A JSON-encoded set of resources to move. Each type is a list of ids. Only folders and items may be specified. For example: {"item": [(item id 1), (item id2)], "folder": [(folder id 1)]}.' schema: type: string - name: parentType in: query required: true description: Parent type for the new parent of these resources. schema: type: string enum: - user - collection - folder - name: parentId in: query required: true description: Parent ID for the new parent of these resources. schema: type: string - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false responses: '200': description: Success '400': description: 'Unsupported or unknown resource type. Invalid resources format. Resource type not supported. No resources specified. Resource not found. ID was invalid.' summary: Move a set of items and folders. tags: - resource /resource/path/download/{path}: get: operationId: resource_pathDownload_path_download_path parameters: - name: path in: path required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: Download a resource based on its path tags: - resource /resource/path/redirect/{path}: delete: description: This is significantly less efficient that using /(model)/(id)/..., as the route must validated and tested to that the longest sensible path is used. operationId: resource_pathRedirect_delete_path_redirect_path parameters: - name: path in: path required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: Redirect to a model endpoint based on a resource path tags: - resource get: description: This is significantly less efficient that using /(model)/(id)/..., as the route must validated and tested to that the longest sensible path is used. operationId: resource_pathRedirect_path_redirect_path parameters: - name: path in: path required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: Redirect to a model endpoint based on a resource path tags: - resource post: description: This is significantly less efficient that using /(model)/(id)/..., as the route must validated and tested to that the longest sensible path is used. operationId: resource_pathRedirect_post_path_redirect_path parameters: - name: path in: path required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: Redirect to a model endpoint based on a resource path tags: - resource put: description: This is significantly less efficient that using /(model)/(id)/..., as the route must validated and tested to that the longest sensible path is used. operationId: resource_pathRedirect_put_path_redirect_path parameters: - name: path in: path required: true description: The path of the resource. The path must be an absolute Unix path starting with either "/user/[user name]", for a user's resources or "/collection/[collection name]", for resources under a collection. schema: type: string responses: '200': description: Success '400': description: 'Path is invalid. Path refers to a resource that does not exist.' '403': description: Read access was denied for the resource. summary: Redirect to a model endpoint based on a resource path tags: - resource /resource/paths: post: operationId: resource_getMultipleResourcePaths_post_paths parameters: [] responses: '200': description: Success '400': description: A parameter was invalid. summary: Get resource paths for multiple resources at once. tags: - resource requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: 'A JSON-encoded set of resources to get resource paths.Each type is a list of ids. For example: {"item": [(item id 1), (item id 2)], "folder": [(folder id 1)]}.' /resource/search: get: operationId: resource_search_search parameters: - name: q in: query required: true description: The search query. schema: type: string - name: mode in: query required: false description: The search mode. Can always use either a text search or a prefix-based search. schema: type: string default: text - name: types in: query required: true description: A JSON list of resource types to search for, e.g. ["user", "folder", "item"]. schema: type: string - name: level in: query required: false description: Minimum required access level. schema: type: integer format: int32 default: 0 - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 10 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 responses: '200': description: Success '400': description: Invalid type list format. summary: Search for resources in the system. tags: - resource /resource/{id}: get: operationId: resource_getResource_id parameters: - name: id in: path required: true description: The ID of the resource. schema: type: string - name: type in: query required: true description: The type of the resource (item, file, etc.). schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read access was denied for the resource. summary: Get any resource by ID. tags: - resource /resource/{id}/items: get: operationId: resource_getResourceItems_id_items parameters: - name: id in: path required: true description: The ID of the resource. schema: type: string - name: type in: query required: true description: The type of the resource (folder, collection, or user). schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: _id - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: ID was invalid. '403': description: Access was denied for the resource. summary: Get all of the items that are children of a resource. tags: - resource /resource/{id}/path: get: operationId: resource_path_id_path parameters: - name: id in: path required: true description: The ID of the resource. schema: type: string - name: type in: query required: true description: The type of the resource (item, file, etc.). schema: type: string responses: '200': description: Success '400': description: 'ID was invalid. Invalid resource type.' '403': description: Read access was denied for the resource. summary: Get path of a resource. tags: - resource /resource/{id}/timestamp: put: operationId: resource_setTimestamp_put_id_timestamp parameters: - name: id in: path required: true description: The ID of the resource. schema: type: string - name: type in: query required: true description: The type of the resource (item, file, etc.). schema: type: string - name: created in: query required: false description: The new created timestamp. schema: type: string - name: updated in: query required: false description: The new updated timestamp. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Access was denied for the resource. summary: Set the created or updated timestamp for a resource. tags: - resource /slicer_cli_web/cli: get: operationId: slicer_cli_web_getItems_cli parameters: - name: folder in: query required: false description: The base folder to look for tasks schema: type: string responses: '200': description: Success '403': description: You are not logged in. summary: List CLIs tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ecf/rerun: post: description: 'Rerun a previous job: Description:

Unmixes the stains of a composite image given the stain colors

Version: 0.2.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ecf_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image to be deconvolved' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image to be deconvolved' schema: type: string - name: outputStainImageFile_1_folder in: query required: false description: 'Girder ID of parent folder for output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string - name: outputStainImageFile_1 in: query required: false description: 'Name of output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string - name: outputStainImageFile_2_folder in: query required: false description: 'Girder ID of parent folder for output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string - name: outputStainImageFile_2 in: query required: false description: 'Name of output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string - name: outputStainImageFile_3_folder in: query required: false description: 'Girder ID of parent folder for output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string - name: outputStainImageFile_3 in: query required: false description: 'Name of output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string - name: maxRegionSize in: query required: false description: Maximum width and height allowed when processing an image, in order to prevent accidentally running on too large a region. Use -1 for no limit schema: type: integer format: int32 - name: region in: query required: false description: left,top,width,height of the region of interest. All -1 means the whole image is used. as JSON (region) schema: type: string - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - 'null' - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ecf/run: post: description: 'Description:

Unmixes the stains of a composite image given the stain colors

Version: 0.2.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ecf_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image to be deconvolved' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image to be deconvolved' schema: type: string - name: outputStainImageFile_1_folder in: query required: true description: 'Girder ID of parent folder for output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string - name: outputStainImageFile_1 in: query required: true description: 'Name of output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string default: outputStainImageFile_1.tiff - name: outputStainImageFile_2_folder in: query required: true description: 'Girder ID of parent folder for output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string - name: outputStainImageFile_2 in: query required: true description: 'Name of output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string default: outputStainImageFile_2.tiff - name: outputStainImageFile_3_folder in: query required: true description: 'Girder ID of parent folder for output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string - name: outputStainImageFile_3 in: query required: true description: 'Name of output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string default: outputStainImageFile_3.tiff - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: maxRegionSize in: query required: false description: Maximum width and height allowed when processing an image, in order to prevent accidentally running on too large a region. Use -1 for no limit schema: type: integer format: int32 default: 5000 - name: region in: query required: false description: left,top,width,height of the region of interest. All -1 means the whole image is used. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - 'null' default: eosin - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom default: 'null' - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' responses: '200': description: Success '400': description: A parameter was invalid. summary: Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed1/rerun: post: description: 'Rerun a previous job: Description:

Use sparse non-negative matrix factorization to adaptively deconvolve a given RGB image into intensity images representing distinct stains.

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed1_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: sample_slide_path in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Input image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Input image to be deconvolved' schema: type: string - name: snmf_I_0 in: query required: false description: Background intensity in each channel as JSON (double-vector) schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: snmf_beta in: query required: false description: A parameter to control sparsity of stain concentrations schema: type: number format: double - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float - name: stains_stain_1 in: query required: false description: Name for initial estimate of color of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stains_stain_1_vector in: query required: false description: Custom value for initial estimate of stain-1 as JSON (double-vector) schema: type: string - name: stains_stain_2 in: query required: false description: Name for initial estimate of color of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stains_stain_2_vector in: query required: false description: Custom value for initial estimate of stain-2 as JSON (double-vector) schema: type: string - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Adaptive Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed1/run: post: description: 'Description:

Use sparse non-negative matrix factorization to adaptively deconvolve a given RGB image into intensity images representing distinct stains.

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed1_run parameters: - name: sample_slide_path in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Input image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Input image to be deconvolved' schema: type: string - name: snmf_I_0 in: query required: true description: Background intensity in each channel as JSON (double-vector) schema: type: string default: '[255.0, 255.0, 255.0]' - name: outputAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: true description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: snmf_beta in: query required: false description: A parameter to control sparsity of stain concentrations schema: type: number format: double default: 0.5 - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float default: -1.0 - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float default: 0.1 - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 default: -1 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float default: 0.1 - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float default: 1.25 - name: stains_stain_1 in: query required: false description: Name for initial estimate of color of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stains_stain_1_vector in: query required: false description: Custom value for initial estimate of stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stains_stain_2 in: query required: false description: Name for initial estimate of color of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom default: eosin - name: stains_stain_2_vector in: query required: false description: Custom value for initial estimate of stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 default: 256 responses: '200': description: Success '400': description: A parameter was invalid. summary: Adaptive Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed3/rerun: post: description: 'Rerun a previous job: Description:

Detects nuclei in a whole-slide image

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed3_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: false description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean - name: ImageInversionForm in: query required: false description: Image inversion may be needed for greyscale images with bright nuclei and dark background. default option will automatically invert the image if it is single channel. Choose if color inversion is needed. schema: type: string enum: - 'Yes' - 'No' - default - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: integer format: int32 - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Detects Nuclei tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed3/run: post: description: 'Description:

Detects nuclei in a whole-slide image

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed3_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: true description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string default: outputNucleiAnnotationFile.anot - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double default: 20.0 - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double default: 1024.0 - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double default: 60.0 - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string default: '{#control:#current_image_frame#}' - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean default: false - name: ImageInversionForm in: query required: false description: Image inversion may be needed for greyscale images with bright nuclei and dark background. default option will automatically invert the image if it is single channel. Choose if color inversion is needed. schema: type: string enum: - 'Yes' - 'No' - default default: default - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double default: 10.0 - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double default: 20.0 - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double default: 0.25 - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: integer format: int32 default: 80 - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double default: 6.0 - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary default: boundary - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 default: 1 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[8.63234435, -0.11501964, 0.03868433]' - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[0.57506023, 0.10403329, 0.01364062]' - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean default: true - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom default: eosin - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom default: 'null' - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string default: '{#control:#current_image_style#}' - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Detects Nuclei tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed5/rerun: post: description: 'Rerun a previous job: Description:

Computes features for nuclei classification

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Sanghoon Lee (Emory University)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed5_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiFeatureFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string - name: outputNucleiFeatureFile in: query required: false description: 'Name of output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: false description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double - name: cyto_width in: query required: false description: Width of ring-like neighborhood region around each nucleus to be considered as cytoplasm schema: type: integer format: int32 - name: cytoplasm_features in: query required: false description: Compute Intensity and Gradient features from the cytoplasm channel schema: type: boolean - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double - name: fsd_features in: query required: false description: Compute Fourier Shape Descriptor Features schema: type: boolean - name: fsd_bnd_pts in: query required: false description: Number of boundary points for computing FSD features schema: type: integer format: int32 - name: fsd_freq_bins in: query required: false description: Number of frequency bins for calculating FSD features schema: type: integer format: int32 - name: gradient_features in: query required: false description: Compute Gradient/Edge Features schema: type: boolean - name: haralick_features in: query required: false description: Compute Haralick Texture Features schema: type: boolean - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean - name: in_annotations in: query required: false description: A comma-separated list of column titles to include in the user attributes of output annotation elements. Blank for none schema: type: string - name: intensity_features in: query required: false description: Compute Intensity Features schema: type: boolean - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: number format: double - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double - name: morphometry_features in: query required: false description: Compute Morphometry (Size and Shape) Features schema: type: boolean - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary - name: num_glcm_levels in: query required: false description: Number of GLCM intensity levels (used to compute haralick features) schema: type: integer format: int32 - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean - name: scheduler in: query required: false description: Address of the dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a cluster on the local machine schema: type: string - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Computes Nuclei Features tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed5/run: post: description: 'Description:

Computes features for nuclei classification

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Sanghoon Lee (Emory University)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed5_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiFeatureFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string - name: outputNucleiFeatureFile in: query required: true description: 'Name of output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string default: outputNucleiFeatureFile.csv - name: outputNucleiAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: true description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string default: outputNucleiAnnotationFile.anot - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double default: 20.0 - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double default: 1024.0 - name: cyto_width in: query required: false description: Width of ring-like neighborhood region around each nucleus to be considered as cytoplasm schema: type: integer format: int32 default: 8 - name: cytoplasm_features in: query required: false description: Compute Intensity and Gradient features from the cytoplasm channel schema: type: boolean default: true - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double default: 60.0 - name: fsd_features in: query required: false description: Compute Fourier Shape Descriptor Features schema: type: boolean default: true - name: fsd_bnd_pts in: query required: false description: Number of boundary points for computing FSD features schema: type: integer format: int32 default: 128 - name: fsd_freq_bins in: query required: false description: Number of frequency bins for calculating FSD features schema: type: integer format: int32 default: 6 - name: gradient_features in: query required: false description: Compute Gradient/Edge Features schema: type: boolean default: true - name: haralick_features in: query required: false description: Compute Haralick Texture Features schema: type: boolean default: true - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean default: false - name: in_annotations in: query required: false description: A comma-separated list of column titles to include in the user attributes of output annotation elements. Blank for none schema: type: string default: Feature.Size.Area,Feature.Size.MajorAxisLength,Feature.Size.MinorAxisLength,Feature.Shape.Circularity,Feature.Shape.Eccentricity,Feature.Nucleus.Intensity.Mean,Feature.Nucleus.Band0.Intensity.Mean,Feature.Nucleus.Band1.Intensity.Mean,Feature.Nucleus.Band2.Intensity.Mean - name: intensity_features in: query required: false description: Compute Intensity Features schema: type: boolean default: true - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double default: 10.0 - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double default: 20.0 - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double default: 0.25 - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: number format: double default: 80.0 - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double default: 6.0 - name: morphometry_features in: query required: false description: Compute Morphometry (Size and Shape) Features schema: type: boolean default: true - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary default: boundary - name: num_glcm_levels in: query required: false description: Number of GLCM intensity levels (used to compute haralick features) schema: type: integer format: int32 default: 32 - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 default: 1 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[8.63234435, -0.11501964, 0.03868433]' - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[0.57506023, 0.10403329, 0.01364062]' - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean default: true - name: scheduler in: query required: false description: Address of the dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a cluster on the local machine schema: type: string default: '' - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom default: eosin - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom default: 'null' - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Computes Nuclei Features tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed7/rerun: post: description: 'Rerun a previous job: Description:

Classify nuclei in an image based on pre-computed features

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware), Subin Erattakulangara (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed7_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image file' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image file' schema: type: string - name: inputModelFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: inputModelFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string - name: outputNucleiAnnotationFile in: query required: false description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string - name: inputNucleiAnnotationFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiFeatureFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: inputNucleiFeatureFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Classify Nuclei tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed7/run: post: description: 'Description:

Classify nuclei in an image based on pre-computed features

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware), Subin Erattakulangara (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed7_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image file' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image file' schema: type: string - name: inputModelFile in: query required: true description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: inputModelFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string - name: outputNucleiAnnotationFile in: query required: true description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string default: outputNucleiAnnotationFile.anot - name: inputNucleiAnnotationFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiFeatureFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: inputNucleiFeatureFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' responses: '200': description: Success '400': description: A parameter was invalid. summary: Classify Nuclei tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed9/rerun: post: description: 'Rerun a previous job: Description:

Sample the background of a slide to compute the median background intensity.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed9_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: slide_path in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string - name: magnification in: query required: false description: Desired magnification for sampling. schema: type: number format: float - name: min_coverage in: query required: false description: Minimum background coverage required for a tile to be sampled from. schema: type: number format: float - name: sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 - name: sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float - name: tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Compute Background Intensity tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566ed9/run: post: description: 'Description:

Sample the background of a slide to compute the median background intensity.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed9_run parameters: - name: slide_path in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: outputAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: true description: 'Name of output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: magnification in: query required: false description: Desired magnification for sampling. schema: type: number format: float default: 1.25 - name: min_coverage in: query required: false description: Minimum background coverage required for a tile to be sampled from. schema: type: number format: float default: 0.1 - name: sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 default: -1 - name: sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float default: 0.1 - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float default: 1.25 - name: tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 default: 256 responses: '200': description: Success '400': description: A parameter was invalid. summary: Compute Background Intensity tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566edb/rerun: post: description: 'Rerun a previous job: Description:

Sample the foreground of a slide to compute the stain vectors using the Macenko method.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566edb_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: sample_slide_path in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: macenko_I_0 in: query required: false description: Background intensity in each channel as JSON (double-vector) schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float - name: macenko_max_angle_percentile in: query required: false description: The larger percentile of one of the vectors to pick from the angle distribution schema: type: number format: double - name: macenko_min_angle_percentile in: query required: false description: The smaller percentile of one of the vectors to pick from the angle distribution schema: type: number format: double - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float - name: macenko_minimum_magnitude in: query required: false description: The magnitude below which vectors will be excluded from the computation of the angle distribution schema: type: number format: double - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Separate Stains (PCA-based Macenko method) tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566edb/run: post: description: 'Description:

Sample the foreground of a slide to compute the stain vectors using the Macenko method.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566edb_run parameters: - name: sample_slide_path in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: macenko_I_0 in: query required: true description: Background intensity in each channel as JSON (double-vector) schema: type: string - name: outputAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: true description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float default: -1.0 - name: macenko_max_angle_percentile in: query required: false description: The larger percentile of one of the vectors to pick from the angle distribution schema: type: number format: double default: 0.99 - name: macenko_min_angle_percentile in: query required: false description: The smaller percentile of one of the vectors to pick from the angle distribution schema: type: number format: double default: 0.01 - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float default: 0.1 - name: macenko_minimum_magnitude in: query required: false description: The magnitude below which vectors will be excluded from the computation of the angle distribution schema: type: number format: double default: 16.0 - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 default: -1 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float default: -1.0 - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float default: 1.25 - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 default: 256 responses: '200': description: Success '400': description: A parameter was invalid. summary: Separate Stains (PCA-based Macenko method) tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566edd/rerun: post: description: 'Rerun a previous job: Description:

Counts different types of positive pixels based on values in the HSI color space

Version: 0.1.0

License: Apache 2.0

Author(s): David Manthey (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566edd_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: hue_value in: query required: false description: Center of the hue range in HSI space for the positive color, in the range [0, 1] schema: type: number format: float - name: hue_width in: query required: false description: Width of the hue range in HSI space schema: type: number format: float - name: saturation_minimum in: query required: false description: Minimum saturation of positive pixels in HSI space, in the range [0, 1] schema: type: number format: float - name: intensity_upper_limit in: query required: false description: Intensity threshold in HSI space above which a pixel is considered negative, in the range [0, 1] schema: type: number format: float - name: intensity_weak_threshold in: query required: false description: Intensity threshold in HSI space that separates weak-positive pixels (above) from plain positive pixels (below) schema: type: number format: float - name: intensity_strong_threshold in: query required: false description: Intensity threshold in HSI space that separates plain positive pixels (above) from strong positive pixels (below) schema: type: number format: float - name: intensity_lower_limit in: query required: false description: Intensity threshold in HSI space below which a pixel is considered negative schema: type: number format: float - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: outputLabelImage_folder in: query required: false description: 'Girder ID of parent folder for output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string - name: outputLabelImage in: query required: false description: 'Name of output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string - name: outputImageForm in: query required: false description: The output image can either be colored for easy visibility or coded as categorical values where 0 is negative, 1 weak, 2 plain, and 3 strong schema: type: string enum: - visible - pixelmap - name: region in: query required: false description: Region of interest where analysis is performed. This is either -1,-1,-1,-1 for the whole image, or a four-element vector in the format "left, top, width, height", or a list of four or more x,y vertices to specify a polygon. as JSON (region) schema: type: string - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Positive Pixel Count tags: - slicer_cli_web /slicer_cli_web/cli/5f3d811c50cd9fe632566edd/run: post: description: 'Description:

Counts different types of positive pixels based on values in the HSI color space

Version: 0.1.0

License: Apache 2.0

Author(s): David Manthey (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566edd_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: hue_value in: query required: true description: Center of the hue range in HSI space for the positive color, in the range [0, 1] schema: type: number format: float default: 0.83 - name: hue_width in: query required: true description: Width of the hue range in HSI space schema: type: number format: float default: 0.15 - name: saturation_minimum in: query required: true description: Minimum saturation of positive pixels in HSI space, in the range [0, 1] schema: type: number format: float default: 0.05 - name: intensity_upper_limit in: query required: true description: Intensity threshold in HSI space above which a pixel is considered negative, in the range [0, 1] schema: type: number format: float default: 0.95 - name: intensity_weak_threshold in: query required: true description: Intensity threshold in HSI space that separates weak-positive pixels (above) from plain positive pixels (below) schema: type: number format: float default: 0.65 - name: intensity_strong_threshold in: query required: true description: Intensity threshold in HSI space that separates plain positive pixels (above) from strong positive pixels (below) schema: type: number format: float default: 0.35 - name: intensity_lower_limit in: query required: true description: Intensity threshold in HSI space below which a pixel is considered negative schema: type: number format: float default: 0.05 - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string default: '{#control:#current_image_frame#}' - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 default: 1 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: outputLabelImage_folder in: query required: false description: 'Girder ID of parent folder for output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string - name: outputLabelImage in: query required: false description: 'Name of output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string default: outputLabelImage.tiff - name: outputImageForm in: query required: false description: The output image can either be colored for easy visibility or coded as categorical values where 0 is negative, 1 weak, 2 plain, and 3 strong schema: type: string enum: - visible - pixelmap default: visible - name: region in: query required: false description: Region of interest where analysis is performed. This is either -1,-1,-1,-1 for the whole image, or a four-element vector in the format "left, top, width, height", or a list of four or more x,y vertices to specify a polygon. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string default: '{#control:#current_image_style#}' responses: '200': description: Success '400': description: A parameter was invalid. summary: Positive Pixel Count tags: - slicer_cli_web /slicer_cli_web/cli/6226c700ea96453654b57afd/rerun: post: description: 'Rerun a previous job: Description:

Create a pixelmap image of superpixels using SLIC.

Version: 0.1.0

License: Apache 2.0

Author(s): Kitware

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_cli_6226c700ea96453654b57afd_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: outputImageFile_folder in: query required: false description: 'Girder ID of parent folder for output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string - name: outputImageFile in: query required: false description: 'Name of output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string - name: boundaries in: query required: false description: Mark the boundary around each superpixel. Boundaries are specified with a separate pixelmap index value that is always 1 higher than the pixelmap index value of the superpixel's interior. schema: type: boolean - name: bounding in: query required: false description: If specified, output an annotation with the bounding box of each superpixel. Internal adds a user.bbox field as a single array to the superpixel annotation with the base image coordinates left,top,right,bottom for each superpixel. schema: type: string enum: - None - Separate - Internal - All - name: compactness in: query required: false description: Balances color proximity and space proximity. Higher values give more weight to space proximity, making superpixel shapes more square/cubic. schema: type: number format: float - name: default_category_label in: query required: false description: Default category label used for superpixels schema: type: string - name: default_fillColor in: query required: false description: Default color for superpixels schema: type: string - name: default_strokeColor in: query required: false description: If creating boundary superpixels, this is the default color of the boundaries of the superpixels schema: type: string - name: magnification in: query required: false description: If specified, the magnification that should be used for the superpixels. If 0, the base magnfication is used schema: type: number format: float - name: overlap in: query required: false description: If specified, overlap tile computation to avoid edge effects. schema: type: boolean - name: roi in: query required: false description: Region of interest within which the analysis should be run as JSON (region) schema: type: string - name: sigma in: query required: false description: Width of Gaussian smoothing kernel for pre-processing for each dimension of the image. The same sigma is applied to each dimension in case of a scalar value. Zero means no smoothing. schema: type: number format: float - name: slic_zero in: query required: false description: If true, run the algorithm in SLIC0 mode to adaptively determine compactness for each superpixel. schema: type: boolean - name: superpixelSize in: query required: false description: Approximate diameter of the average superpixel. schema: type: integer format: int32 - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string - name: tileSize in: query required: false description: Specify the size of the working tile. If there is no overlap, superpixel boundaries will appear at these locations. schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Superpixel Pixelmap tags: - slicer_cli_web /slicer_cli_web/cli/6226c700ea96453654b57afd/run: post: description: 'Description:

Create a pixelmap image of superpixels using SLIC.

Version: 0.1.0

License: Apache 2.0

Author(s): Kitware

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_cli_6226c700ea96453654b57afd_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: outputImageFile_folder in: query required: true description: 'Girder ID of parent folder for output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string - name: outputImageFile in: query required: true description: 'Name of output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string default: outputImageFile.tiff - name: boundaries in: query required: false description: Mark the boundary around each superpixel. Boundaries are specified with a separate pixelmap index value that is always 1 higher than the pixelmap index value of the superpixel's interior. schema: type: boolean default: true - name: bounding in: query required: false description: If specified, output an annotation with the bounding box of each superpixel. Internal adds a user.bbox field as a single array to the superpixel annotation with the base image coordinates left,top,right,bottom for each superpixel. schema: type: string enum: - None - Separate - Internal - All default: None - name: compactness in: query required: false description: Balances color proximity and space proximity. Higher values give more weight to space proximity, making superpixel shapes more square/cubic. schema: type: number format: float default: 1.0 - name: default_category_label in: query required: false description: Default category label used for superpixels schema: type: string default: default - name: default_fillColor in: query required: false description: Default color for superpixels schema: type: string default: rgba(0, 0, 0, 0) - name: default_strokeColor in: query required: false description: If creating boundary superpixels, this is the default color of the boundaries of the superpixels schema: type: string default: rgba(0, 0, 0, 1) - name: magnification in: query required: false description: If specified, the magnification that should be used for the superpixels. If 0, the base magnfication is used schema: type: number format: float default: 0.0 - name: overlap in: query required: false description: If specified, overlap tile computation to avoid edge effects. schema: type: boolean default: false - name: roi in: query required: false description: Region of interest within which the analysis should be run as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: sigma in: query required: false description: Width of Gaussian smoothing kernel for pre-processing for each dimension of the image. The same sigma is applied to each dimension in case of a scalar value. Zero means no smoothing. schema: type: number format: float default: 0.0 - name: slic_zero in: query required: false description: If true, run the algorithm in SLIC0 mode to adaptively determine compactness for each superpixel. schema: type: boolean default: true - name: superpixelSize in: query required: false description: Approximate diameter of the average superpixel. schema: type: integer format: int32 default: 50 - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: tileSize in: query required: false description: Specify the size of the working tile. If there is no overlap, superpixel boundaries will appear at these locations. schema: type: integer format: int32 default: 4096 responses: '200': description: Success '400': description: A parameter was invalid. summary: Superpixel Pixelmap tags: - slicer_cli_web /slicer_cli_web/cli/63a0a1fd9a9ebb3f668acd34/rerun: post: description: 'Rerun a previous job: Description:

Simple Get Region

Version: 0.1.0

License: Apache 2.0

Author(s): David Gutman and Jc Vizcarra' operationId: slicer_cli_web_rerunHandler_post_cli_63a0a1fd9a9ebb3f668acd34_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: in_file in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - in_file: Input image' schema: type: string - name: in_file_folder in: query required: false description: 'Girder ID of parent folder for batch input image - in_file: Input image' schema: type: string - name: mag in: query required: false description: Output thumbnail magnification schema: type: number format: float - name: out_file_folder in: query required: false description: 'Girder ID of parent folder for output image - out_file: Output Region Image file' schema: type: string - name: out_file in: query required: false description: 'Name of output image - out_file: Output Region Image file' schema: type: string - name: girderApiUrl in: query required: false description: A Girder API URL (e.g., https://girder.example.com:443/api/v1) schema: type: string - name: girderToken in: query required: false description: A Girder token schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Simple Get Region tags: - slicer_cli_web /slicer_cli_web/cli/63a0a1fd9a9ebb3f668acd34/run: post: description: 'Description:

Simple Get Region

Version: 0.1.0

License: Apache 2.0

Author(s): David Gutman and Jc Vizcarra' operationId: slicer_cli_web_cliHandler_post_cli_63a0a1fd9a9ebb3f668acd34_run parameters: - name: in_file in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - in_file: Input image' schema: type: string - name: in_file_folder in: query required: false description: 'Girder ID of parent folder for batch input image - in_file: Input image' schema: type: string - name: mag in: query required: true description: Output thumbnail magnification schema: type: number format: float - name: out_file_folder in: query required: true description: 'Girder ID of parent folder for output image - out_file: Output Region Image file' schema: type: string - name: out_file in: query required: true description: 'Name of output image - out_file: Output Region Image file' schema: type: string default: out_file.nrrd - name: girderApiUrl in: query required: false description: A Girder API URL (e.g., https://girder.example.com:443/api/v1) schema: type: string default: '' - name: girderToken in: query required: false description: A Girder token schema: type: string default: '' responses: '200': description: Success '400': description: A parameter was invalid. summary: Simple Get Region tags: - slicer_cli_web /slicer_cli_web/cli/{id}: delete: operationId: slicer_cli_web_deleteItem_delete_cli_id parameters: - name: id in: path required: true description: The task item schema: type: string responses: '200': description: Success '403': description: You are not logged in. summary: Get a specific CLI tags: - slicer_cli_web get: operationId: slicer_cli_web_getItem_cli_id parameters: - name: id in: path required: true description: The task item schema: type: string responses: '200': description: Success '403': description: You are not logged in. summary: Get a specific CLI tags: - slicer_cli_web /slicer_cli_web/cli/{id}/xml: get: operationId: slicer_cli_web_getItemXML_cli_id_xml parameters: - name: id in: path required: true description: The task item schema: type: string responses: '200': description: Success '403': description: You are not logged in. summary: Get a specific CLI tags: - slicer_cli_web /slicer_cli_web/docker_image: delete: description: Must be a system administrator to call this. operationId: slicer_cli_web_deleteImage_delete_docker_image parameters: - name: name in: query required: true description: The name or a list of names of the docker images to be removed schema: type: string - name: delete_from_local_repo in: query required: false description: If True the image is deleted from the local repo, requiring it to be pulled from a remote repository the next time it is used. If False the metadata regarding the image is deleted, but the docker image remains. schema: type: boolean default: false responses: '200': description: Success '403': description: You are not a system administrator. '500': description: Failed to set system setting. summary: Remove a docker image tags: - slicer_cli_web get: description: You must be logged in to see any results. operationId: slicer_cli_web_getDockerImages_docker_image responses: '200': description: Success '400': description: A parameter was invalid. summary: List docker images and their CLIs tags: - slicer_cli_web parameters: [] put: description: Must be a system administrator to call this. operationId: slicer_cli_web_setImages_put_docker_image parameters: - name: name in: query required: true description: A name or a list of names of the docker images to be loaded schema: type: string - name: folder in: query required: false description: The base folder id to upload the tasks to schema: type: string - name: pull in: query required: false description: If True, try to repull all images schema: type: string responses: '200': description: Success '403': description: You are not a system administrator. '500': description: Failed to set system setting. summary: Add one or a list of images tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/BackgroundIntensity/rerun: post: description: 'Rerun a previous job: Description:

Sample the background of a slide to compute the median background intensity.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_BackgroundIntensity_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: slide_path in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string - name: magnification in: query required: false description: Desired magnification for sampling. schema: type: number format: float - name: min_coverage in: query required: false description: Minimum background coverage required for a tile to be sampled from. schema: type: number format: float - name: sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 - name: sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float - name: tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Compute Background Intensity tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/BackgroundIntensity/run: post: description: 'Description:

Sample the background of a slide to compute the median background intensity.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_BackgroundIntensity_run parameters: - name: slide_path in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - slide_path: Path to input slide image to be deconvolved' schema: type: string - name: outputAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: true description: 'Name of output file - outputAnnotationFile: Output intensity in SDA space (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: magnification in: query required: false description: Desired magnification for sampling. schema: type: number format: float default: 1.25 - name: min_coverage in: query required: false description: Minimum background coverage required for a tile to be sampled from. schema: type: number format: float default: 0.1 - name: sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 default: -1 - name: sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float default: 0.1 - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float default: 1.25 - name: tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 default: 256 responses: '200': description: Success '400': description: A parameter was invalid. summary: Compute Background Intensity tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/ColorDeconvolution/rerun: post: description: 'Rerun a previous job: Description:

Unmixes the stains of a composite image given the stain colors

Version: 0.2.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_ColorDeconvolution_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image to be deconvolved' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image to be deconvolved' schema: type: string - name: outputStainImageFile_1_folder in: query required: false description: 'Girder ID of parent folder for output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string - name: outputStainImageFile_1 in: query required: false description: 'Name of output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string - name: outputStainImageFile_2_folder in: query required: false description: 'Girder ID of parent folder for output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string - name: outputStainImageFile_2 in: query required: false description: 'Name of output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string - name: outputStainImageFile_3_folder in: query required: false description: 'Girder ID of parent folder for output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string - name: outputStainImageFile_3 in: query required: false description: 'Name of output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string - name: maxRegionSize in: query required: false description: Maximum width and height allowed when processing an image, in order to prevent accidentally running on too large a region. Use -1 for no limit schema: type: integer format: int32 - name: region in: query required: false description: left,top,width,height of the region of interest. All -1 means the whole image is used. as JSON (region) schema: type: string - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - 'null' - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/ColorDeconvolution/run: post: description: 'Description:

Unmixes the stains of a composite image given the stain colors

Version: 0.2.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_ColorDeconvolution_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image to be deconvolved' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image to be deconvolved' schema: type: string - name: outputStainImageFile_1_folder in: query required: true description: 'Girder ID of parent folder for output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string - name: outputStainImageFile_1 in: query required: true description: 'Name of output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)' schema: type: string default: outputStainImageFile_1.tiff - name: outputStainImageFile_2_folder in: query required: true description: 'Girder ID of parent folder for output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string - name: outputStainImageFile_2 in: query required: true description: 'Name of output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)' schema: type: string default: outputStainImageFile_2.tiff - name: outputStainImageFile_3_folder in: query required: true description: 'Girder ID of parent folder for output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string - name: outputStainImageFile_3 in: query required: true description: 'Name of output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)' schema: type: string default: outputStainImageFile_3.tiff - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate images on source (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: maxRegionSize in: query required: false description: Maximum width and height allowed when processing an image, in order to prevent accidentally running on too large a region. Use -1 for no limit schema: type: integer format: int32 default: 5000 - name: region in: query required: false description: left,top,width,height of the region of interest. All -1 means the whole image is used. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - 'null' default: eosin - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom default: 'null' - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' responses: '200': description: Success '400': description: A parameter was invalid. summary: Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/ComputeNucleiFeatures/rerun: post: description: 'Rerun a previous job: Description:

Computes features for nuclei classification

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Sanghoon Lee (Emory University)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_ComputeNucleiFeatures_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiFeatureFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string - name: outputNucleiFeatureFile in: query required: false description: 'Name of output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: false description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double - name: cyto_width in: query required: false description: Width of ring-like neighborhood region around each nucleus to be considered as cytoplasm schema: type: integer format: int32 - name: cytoplasm_features in: query required: false description: Compute Intensity and Gradient features from the cytoplasm channel schema: type: boolean - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double - name: fsd_features in: query required: false description: Compute Fourier Shape Descriptor Features schema: type: boolean - name: fsd_bnd_pts in: query required: false description: Number of boundary points for computing FSD features schema: type: integer format: int32 - name: fsd_freq_bins in: query required: false description: Number of frequency bins for calculating FSD features schema: type: integer format: int32 - name: gradient_features in: query required: false description: Compute Gradient/Edge Features schema: type: boolean - name: haralick_features in: query required: false description: Compute Haralick Texture Features schema: type: boolean - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean - name: in_annotations in: query required: false description: A comma-separated list of column titles to include in the user attributes of output annotation elements. Blank for none schema: type: string - name: intensity_features in: query required: false description: Compute Intensity Features schema: type: boolean - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: number format: double - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double - name: morphometry_features in: query required: false description: Compute Morphometry (Size and Shape) Features schema: type: boolean - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary - name: num_glcm_levels in: query required: false description: Number of GLCM intensity levels (used to compute haralick features) schema: type: integer format: int32 - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean - name: scheduler in: query required: false description: Address of the dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a cluster on the local machine schema: type: string - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Computes Nuclei Features tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/ComputeNucleiFeatures/run: post: description: 'Description:

Computes features for nuclei classification

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Sanghoon Lee (Emory University)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_ComputeNucleiFeatures_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiFeatureFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string - name: outputNucleiFeatureFile in: query required: true description: 'Name of output file - outputNucleiFeatureFile: Output nuclei feature file (*.csv or *.h5)' schema: type: string default: outputNucleiFeatureFile.csv - name: outputNucleiAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: true description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string default: outputNucleiAnnotationFile.anot - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double default: 20.0 - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double default: 1024.0 - name: cyto_width in: query required: false description: Width of ring-like neighborhood region around each nucleus to be considered as cytoplasm schema: type: integer format: int32 default: 8 - name: cytoplasm_features in: query required: false description: Compute Intensity and Gradient features from the cytoplasm channel schema: type: boolean default: true - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double default: 60.0 - name: fsd_features in: query required: false description: Compute Fourier Shape Descriptor Features schema: type: boolean default: true - name: fsd_bnd_pts in: query required: false description: Number of boundary points for computing FSD features schema: type: integer format: int32 default: 128 - name: fsd_freq_bins in: query required: false description: Number of frequency bins for calculating FSD features schema: type: integer format: int32 default: 6 - name: gradient_features in: query required: false description: Compute Gradient/Edge Features schema: type: boolean default: true - name: haralick_features in: query required: false description: Compute Haralick Texture Features schema: type: boolean default: true - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean default: false - name: in_annotations in: query required: false description: A comma-separated list of column titles to include in the user attributes of output annotation elements. Blank for none schema: type: string default: Feature.Size.Area,Feature.Size.MajorAxisLength,Feature.Size.MinorAxisLength,Feature.Shape.Circularity,Feature.Shape.Eccentricity,Feature.Nucleus.Intensity.Mean,Feature.Nucleus.Band0.Intensity.Mean,Feature.Nucleus.Band1.Intensity.Mean,Feature.Nucleus.Band2.Intensity.Mean - name: intensity_features in: query required: false description: Compute Intensity Features schema: type: boolean default: true - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double default: 10.0 - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double default: 20.0 - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double default: 0.25 - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: number format: double default: 80.0 - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double default: 6.0 - name: morphometry_features in: query required: false description: Compute Morphometry (Size and Shape) Features schema: type: boolean default: true - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary default: boundary - name: num_glcm_levels in: query required: false description: Number of GLCM intensity levels (used to compute haralick features) schema: type: integer format: int32 default: 32 - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 default: 1 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[8.63234435, -0.11501964, 0.03868433]' - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[0.57506023, 0.10403329, 0.01364062]' - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean default: true - name: scheduler in: query required: false description: Address of the dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a cluster on the local machine schema: type: string default: '' - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom default: eosin - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom default: 'null' - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Computes Nuclei Features tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/NucleiClassification/rerun: post: description: 'Rerun a previous job: Description:

Classify nuclei in an image based on pre-computed features

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware), Subin Erattakulangara (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_NucleiClassification_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image file' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image file' schema: type: string - name: inputModelFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: inputModelFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string - name: outputNucleiAnnotationFile in: query required: false description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string - name: inputNucleiAnnotationFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiFeatureFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: inputNucleiFeatureFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Classify Nuclei tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/NucleiClassification/run: post: description: 'Description:

Classify nuclei in an image based on pre-computed features

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware), Subin Erattakulangara (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_NucleiClassification_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image file' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image file' schema: type: string - name: inputModelFile in: query required: true description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: inputModelFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputModelFile: Pickled file (*.pkl) of the scikit-learn model for classifying nuclei' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string - name: outputNucleiAnnotationFile in: query required: true description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot) with the same nuclei in input nuclei annotation file if provided) with nuclei sorted into groups based on class and accompanied by heatmaps of the classification probabilities' schema: type: string default: outputNucleiAnnotationFile.anot - name: inputNucleiAnnotationFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiAnnotationFile: Input nuclei annotation file (*.anot) containing nuclei annotations in the same order as their features in the feature file' schema: type: string - name: inputNucleiFeatureFile in: query required: false description: 'Girder ID of input file (if batch input, this is a regex for item names) - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: inputNucleiFeatureFile_folder in: query required: false description: 'Girder ID of parent folder for batch input file - inputNucleiFeatureFile: Input nuclei feature file (*.csv, *.h5) containing the features of all nuclei to be classified' schema: type: string - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' responses: '200': description: Success '400': description: A parameter was invalid. summary: Classify Nuclei tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/NucleiDetection/rerun: post: description: 'Rerun a previous job: Description:

Detects nuclei in a whole-slide image

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_NucleiDetection_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: false description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean - name: ImageInversionForm in: query required: false description: Image inversion may be needed for greyscale images with bright nuclei and dark background. default option will automatically invert the image if it is single channel. Choose if color inversion is needed. schema: type: string enum: - 'Yes' - 'No' - default - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: integer format: int32 - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Detects Nuclei tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/NucleiDetection/run: post: description: 'Description:

Detects nuclei in a whole-slide image

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_NucleiDetection_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image' schema: type: string - name: outputNucleiAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string - name: outputNucleiAnnotationFile in: query required: true description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)' schema: type: string default: outputNucleiAnnotationFile.anot - name: analysis_mag in: query required: false description: The magnification at which the analysis should be performed. schema: type: number format: double default: 20.0 - name: analysis_roi in: query required: false description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: analysis_tile_size in: query required: false description: Tile size for blockwise analysis schema: type: number format: double default: 1024.0 - name: foreground_threshold in: query required: false description: Intensity value to use as threshold to segment foreground in nuclear stain image schema: type: number format: double default: 60.0 - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string default: '{#control:#current_image_frame#}' - name: ignore_border_nuclei in: query required: false description: Ignore/drop nuclei touching the image/tile border schema: type: boolean default: false - name: ImageInversionForm in: query required: false description: Image inversion may be needed for greyscale images with bright nuclei and dark background. default option will automatically invert the image if it is single channel. Choose if color inversion is needed. schema: type: string enum: - 'Yes' - 'No' - default default: default - name: local_max_search_radius in: query required: false description: Local max search radius used for detection seed points in nuclei schema: type: number format: double default: 10.0 - name: max_radius in: query required: false description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter) schema: type: number format: double default: 20.0 - name: min_fgnd_frac in: query required: false description: The minimum amount of foreground that must be present in a tile for it to be analyzed schema: type: number format: double default: 0.25 - name: min_nucleus_area in: query required: false description: Minimum area that each nucleus should have schema: type: integer format: int32 default: 80 - name: min_radius in: query required: false description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter) schema: type: number format: double default: 6.0 - name: nuclei_annotation_format in: query required: false description: Format of the output nuclei annotations schema: type: string enum: - bbox - boundary default: boundary - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 default: 1 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: reference_mu_lab in: query required: false description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[8.63234435, -0.11501964, 0.03868433]' - name: reference_std_lab in: query required: false description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector) schema: type: string default: '[0.57506023, 0.10403329, 0.01364062]' - name: remove_overlapping_nuclei_segmentation in: query required: false description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter. schema: type: boolean default: true - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: stain_1 in: query required: false description: Name of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stain_1_vector in: query required: false description: Custom value for stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_2 in: query required: false description: Name of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom default: eosin - name: stain_2_vector in: query required: false description: Custom value for stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stain_3 in: query required: false description: Name of stain-3 schema: type: string enum: - hematoxylin - eosin - dab - 'null' - custom default: 'null' - name: stain_3_vector in: query required: false description: Custom value for stain-3 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string default: '{#control:#current_image_style#}' - name: tile_overlap_value in: query required: false description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4 schema: type: integer format: int32 default: -1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Detects Nuclei tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/PositivePixelCount/rerun: post: description: 'Rerun a previous job: Description:

Counts different types of positive pixels based on values in the HSI color space

Version: 0.1.0

License: Apache 2.0

Author(s): David Manthey (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_PositivePixelCount_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: hue_value in: query required: false description: Center of the hue range in HSI space for the positive color, in the range [0, 1] schema: type: number format: float - name: hue_width in: query required: false description: Width of the hue range in HSI space schema: type: number format: float - name: saturation_minimum in: query required: false description: Minimum saturation of positive pixels in HSI space, in the range [0, 1] schema: type: number format: float - name: intensity_upper_limit in: query required: false description: Intensity threshold in HSI space above which a pixel is considered negative, in the range [0, 1] schema: type: number format: float - name: intensity_weak_threshold in: query required: false description: Intensity threshold in HSI space that separates weak-positive pixels (above) from plain positive pixels (below) schema: type: number format: float - name: intensity_strong_threshold in: query required: false description: Intensity threshold in HSI space that separates plain positive pixels (above) from strong positive pixels (below) schema: type: number format: float - name: intensity_lower_limit in: query required: false description: Intensity threshold in HSI space below which a pixel is considered negative schema: type: number format: float - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 - name: outputLabelImage_folder in: query required: false description: 'Girder ID of parent folder for output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string - name: outputLabelImage in: query required: false description: 'Name of output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string - name: outputImageForm in: query required: false description: The output image can either be colored for easy visibility or coded as categorical values where 0 is negative, 1 weak, 2 plain, and 3 strong schema: type: string enum: - visible - pixelmap - name: region in: query required: false description: Region of interest where analysis is performed. This is either -1,-1,-1,-1 for the whole image, or a four-element vector in the format "left, top, width, height", or a list of four or more x,y vertices to specify a polygon. as JSON (region) schema: type: string - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Positive Pixel Count tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/PositivePixelCount/run: post: description: 'Description:

Counts different types of positive pixels based on values in the HSI color space

Version: 0.1.0

License: Apache 2.0

Author(s): David Manthey (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_PositivePixelCount_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image in which to count and classify positive pixels' schema: type: string - name: hue_value in: query required: true description: Center of the hue range in HSI space for the positive color, in the range [0, 1] schema: type: number format: float default: 0.83 - name: hue_width in: query required: true description: Width of the hue range in HSI space schema: type: number format: float default: 0.15 - name: saturation_minimum in: query required: true description: Minimum saturation of positive pixels in HSI space, in the range [0, 1] schema: type: number format: float default: 0.05 - name: intensity_upper_limit in: query required: true description: Intensity threshold in HSI space above which a pixel is considered negative, in the range [0, 1] schema: type: number format: float default: 0.95 - name: intensity_weak_threshold in: query required: true description: Intensity threshold in HSI space that separates weak-positive pixels (above) from plain positive pixels (below) schema: type: number format: float default: 0.65 - name: intensity_strong_threshold in: query required: true description: Intensity threshold in HSI space that separates plain positive pixels (above) from strong positive pixels (below) schema: type: number format: float default: 0.35 - name: intensity_lower_limit in: query required: true description: Intensity threshold in HSI space below which a pixel is considered negative schema: type: number format: float default: 0.05 - name: frame in: query required: false description: Frame index in a multi-frame image schema: type: string default: '{#control:#current_image_frame#}' - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to relate the image to the source (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: num_threads_per_worker in: query required: false description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1. schema: type: integer format: int32 default: 1 - name: num_workers in: query required: false description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified. schema: type: integer format: int32 default: -1 - name: outputLabelImage_folder in: query required: false description: 'Girder ID of parent folder for output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string - name: outputLabelImage in: query required: false description: 'Name of output image - outputLabelImage: Color-coded image of the region, showing the various classes of pixel' schema: type: string default: outputLabelImage.tiff - name: outputImageForm in: query required: false description: The output image can either be colored for easy visibility or coded as categorical values where 0 is negative, 1 weak, 2 plain, and 3 strong schema: type: string enum: - visible - pixelmap default: visible - name: region in: query required: false description: Region of interest where analysis is performed. This is either -1,-1,-1,-1 for the whole image, or a four-element vector in the format "left, top, width, height", or a list of four or more x,y vertices to specify a polygon. as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: style in: query required: false description: Image style options for compositing a multi-frame image schema: type: string default: '{#control:#current_image_style#}' responses: '200': description: Success '400': description: A parameter was invalid. summary: Positive Pixel Count tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/SeparateStainsMacenkoPCA/rerun: post: description: 'Rerun a previous job: Description:

Sample the foreground of a slide to compute the stain vectors using the Macenko method.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_SeparateStainsMacenkoPCA_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: sample_slide_path in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: macenko_I_0 in: query required: false description: Background intensity in each channel as JSON (double-vector) schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float - name: macenko_max_angle_percentile in: query required: false description: The larger percentile of one of the vectors to pick from the angle distribution schema: type: number format: double - name: macenko_min_angle_percentile in: query required: false description: The smaller percentile of one of the vectors to pick from the angle distribution schema: type: number format: double - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float - name: macenko_minimum_magnitude in: query required: false description: The magnitude below which vectors will be excluded from the computation of the angle distribution schema: type: number format: double - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Separate Stains (PCA-based Macenko method) tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/SeparateStainsMacenkoPCA/run: post: description: 'Description:

Sample the foreground of a slide to compute the stain vectors using the Macenko method.

Version: 0.1.0

License: Apache 2.0

Author(s): Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_SeparateStainsMacenkoPCA_run parameters: - name: sample_slide_path in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Path to input slide image to be deconvolved' schema: type: string - name: macenko_I_0 in: query required: true description: Background intensity in each channel as JSON (double-vector) schema: type: string - name: outputAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: true description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float default: -1.0 - name: macenko_max_angle_percentile in: query required: false description: The larger percentile of one of the vectors to pick from the angle distribution schema: type: number format: double default: 0.99 - name: macenko_min_angle_percentile in: query required: false description: The smaller percentile of one of the vectors to pick from the angle distribution schema: type: number format: double default: 0.01 - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float default: 0.1 - name: macenko_minimum_magnitude in: query required: false description: The magnitude below which vectors will be excluded from the computation of the angle distribution schema: type: number format: double default: 16.0 - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 default: -1 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float default: -1.0 - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float default: 1.25 - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 default: 256 responses: '200': description: Success '400': description: A parameter was invalid. summary: Separate Stains (PCA-based Macenko method) tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/SeparateStainsXuSnmf/rerun: post: description: 'Rerun a previous job: Description:

Use sparse non-negative matrix factorization to adaptively deconvolve a given RGB image into intensity images representing distinct stains.

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_SeparateStainsXuSnmf_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: sample_slide_path in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Input image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Input image to be deconvolved' schema: type: string - name: snmf_I_0 in: query required: false description: Background intensity in each channel as JSON (double-vector) schema: type: string - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: snmf_beta in: query required: false description: A parameter to control sparsity of stain concentrations schema: type: number format: double - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float - name: stains_stain_1 in: query required: false description: Name for initial estimate of color of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stains_stain_1_vector in: query required: false description: Custom value for initial estimate of stain-1 as JSON (double-vector) schema: type: string - name: stains_stain_2 in: query required: false description: Name for initial estimate of color of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom - name: stains_stain_2_vector in: query required: false description: Custom value for initial estimate of stain-2 as JSON (double-vector) schema: type: string - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Adaptive Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/SeparateStainsXuSnmf/run: post: description: 'Description:

Use sparse non-negative matrix factorization to adaptively deconvolve a given RGB image into intensity images representing distinct stains.

Version: 0.1.0

License: Apache 2.0

Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_SeparateStainsXuSnmf_run parameters: - name: sample_slide_path in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Input image to be deconvolved' schema: type: string - name: sample_slide_path_folder in: query required: false description: 'Girder ID of parent folder for batch input image - sample_slide_path: Input image to be deconvolved' schema: type: string - name: snmf_I_0 in: query required: true description: Background intensity in each channel as JSON (double-vector) schema: type: string default: '[255.0, 255.0, 255.0]' - name: outputAnnotationFile_folder in: query required: true description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: true description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: snmf_beta in: query required: false description: A parameter to control sparsity of stain concentrations schema: type: number format: double default: 0.5 - name: sample_magnification in: query required: false description: Desired magnification for sampling. The default value indicates native scan magnification. schema: type: number format: float default: -1.0 - name: sample_min_coverage in: query required: false description: "Minimum background coverage required for a tile to\n be sampled from." schema: type: number format: float default: 0.1 - name: sample_sample_approximate_total in: query required: false description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be. schema: type: integer format: int32 default: -1 - name: sample_sample_fraction in: query required: false description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal schema: type: number format: float default: 0.1 - name: dask_scheduler in: query required: false description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode. schema: type: string default: '' - name: sample_tissue_seg_mag in: query required: false description: Low resolution magnification at which foreground and background will be segmented. schema: type: number format: float default: 1.25 - name: stains_stain_1 in: query required: false description: Name for initial estimate of color of stain-1 schema: type: string enum: - hematoxylin - eosin - dab - custom default: hematoxylin - name: stains_stain_1_vector in: query required: false description: Custom value for initial estimate of stain-1 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: stains_stain_2 in: query required: false description: Name for initial estimate of color of stain-2 schema: type: string enum: - hematoxylin - eosin - dab - custom default: eosin - name: stains_stain_2_vector in: query required: false description: Custom value for initial estimate of stain-2 as JSON (double-vector) schema: type: string default: '[-1.0, -1.0, -1.0]' - name: sample_tile_grouping in: query required: false description: Number of tiles to process as part of a single task schema: type: integer format: int32 default: 256 responses: '200': description: Success '400': description: A parameter was invalid. summary: Adaptive Color Deconvolution tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/SuperpixelSegmentation/rerun: post: description: 'Rerun a previous job: Description:

Create a pixelmap image of superpixels using SLIC.

Version: 0.1.0

License: Apache 2.0

Author(s): Kitware

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_rerunHandler_post_dsarchive_histomicstk_latest_SuperpixelSegmentation_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: inputImageFile in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: outputImageFile_folder in: query required: false description: 'Girder ID of parent folder for output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string - name: outputImageFile in: query required: false description: 'Name of output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string - name: boundaries in: query required: false description: Mark the boundary around each superpixel. Boundaries are specified with a separate pixelmap index value that is always 1 higher than the pixelmap index value of the superpixel's interior. schema: type: boolean - name: bounding in: query required: false description: If specified, output an annotation with the bounding box of each superpixel. Internal adds a user.bbox field as a single array to the superpixel annotation with the base image coordinates left,top,right,bottom for each superpixel. schema: type: string enum: - None - Separate - Internal - All - name: compactness in: query required: false description: Balances color proximity and space proximity. Higher values give more weight to space proximity, making superpixel shapes more square/cubic. schema: type: number format: float - name: default_category_label in: query required: false description: Default category label used for superpixels schema: type: string - name: default_fillColor in: query required: false description: Default color for superpixels schema: type: string - name: default_strokeColor in: query required: false description: If creating boundary superpixels, this is the default color of the boundaries of the superpixels schema: type: string - name: magnification in: query required: false description: If specified, the magnification that should be used for the superpixels. If 0, the base magnfication is used schema: type: number format: float - name: overlap in: query required: false description: If specified, overlap tile computation to avoid edge effects. schema: type: boolean - name: roi in: query required: false description: Region of interest within which the analysis should be run as JSON (region) schema: type: string - name: sigma in: query required: false description: Width of Gaussian smoothing kernel for pre-processing for each dimension of the image. The same sigma is applied to each dimension in case of a scalar value. Zero means no smoothing. schema: type: number format: float - name: slic_zero in: query required: false description: If true, run the algorithm in SLIC0 mode to adaptively determine compactness for each superpixel. schema: type: boolean - name: superpixelSize in: query required: false description: Approximate diameter of the average superpixel. schema: type: integer format: int32 - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string - name: tileSize in: query required: false description: Specify the size of the working tile. If there is no overlap, superpixel boundaries will appear at these locations. schema: type: integer format: int32 responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Superpixel Pixelmap tags: - slicer_cli_web /slicer_cli_web/dsarchive_histomicstk_latest/SuperpixelSegmentation/run: post: description: 'Description:

Create a pixelmap image of superpixels using SLIC.

Version: 0.1.0

License: Apache 2.0

Author(s): Kitware

Acknowledgements: This work is part of the HistomicsTK project.' operationId: slicer_cli_web_cliHandler_post_dsarchive_histomicstk_latest_SuperpixelSegmentation_run parameters: - name: inputImageFile in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: inputImageFile_folder in: query required: false description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image for superpixel segmentation' schema: type: string - name: outputImageFile_folder in: query required: true description: 'Girder ID of parent folder for output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string - name: outputImageFile in: query required: true description: 'Name of output image - outputImageFile: Output Image of Superpixel Pixelmap (*.tiff)' schema: type: string default: outputImageFile.tiff - name: boundaries in: query required: false description: Mark the boundary around each superpixel. Boundaries are specified with a separate pixelmap index value that is always 1 higher than the pixelmap index value of the superpixel's interior. schema: type: boolean default: true - name: bounding in: query required: false description: If specified, output an annotation with the bounding box of each superpixel. Internal adds a user.bbox field as a single array to the superpixel annotation with the base image coordinates left,top,right,bottom for each superpixel. schema: type: string enum: - None - Separate - Internal - All default: None - name: compactness in: query required: false description: Balances color proximity and space proximity. Higher values give more weight to space proximity, making superpixel shapes more square/cubic. schema: type: number format: float default: 1.0 - name: default_category_label in: query required: false description: Default category label used for superpixels schema: type: string default: default - name: default_fillColor in: query required: false description: Default color for superpixels schema: type: string default: rgba(0, 0, 0, 0) - name: default_strokeColor in: query required: false description: If creating boundary superpixels, this is the default color of the boundaries of the superpixels schema: type: string default: rgba(0, 0, 0, 1) - name: magnification in: query required: false description: If specified, the magnification that should be used for the superpixels. If 0, the base magnfication is used schema: type: number format: float default: 0.0 - name: overlap in: query required: false description: If specified, overlap tile computation to avoid edge effects. schema: type: boolean default: false - name: roi in: query required: false description: Region of interest within which the analysis should be run as JSON (region) schema: type: string default: '[-1.0, -1.0, -1.0, -1.0]' - name: sigma in: query required: false description: Width of Gaussian smoothing kernel for pre-processing for each dimension of the image. The same sigma is applied to each dimension in case of a scalar value. Zero means no smoothing. schema: type: number format: float default: 0.0 - name: slic_zero in: query required: false description: If true, run the algorithm in SLIC0 mode to adaptively determine compactness for each superpixel. schema: type: boolean default: true - name: superpixelSize in: query required: false description: Approximate diameter of the average superpixel. schema: type: integer format: int32 default: 50 - name: outputAnnotationFile_folder in: query required: false description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string - name: outputAnnotationFile in: query required: false description: 'Name of output file - outputAnnotationFile: Annotation to display pixelmap on source (*.anot)' schema: type: string default: outputAnnotationFile.anot - name: tileSize in: query required: false description: Specify the size of the working tile. If there is no overlap, superpixel boundaries will appear at these locations. schema: type: integer format: int32 default: 4096 responses: '200': description: Success '400': description: A parameter was invalid. summary: Superpixel Pixelmap tags: - slicer_cli_web /slicer_cli_web/jvizcar_braak-study_cli-tasks/hp_tau_detection/rerun: post: description: 'Rerun a previous job: Description:

Simple Get Region

Version: 0.1.0

License: Apache 2.0

Author(s): David Gutman and Jc Vizcarra' operationId: slicer_cli_web_rerunHandler_post_jvizcar_braak-study_cli-tasks_hp_tau_detection_rerun parameters: - name: jobId in: query required: true description: The previous job ID schema: type: string - name: in_file in: query required: false description: 'Girder ID of input image (if batch input, this is a regex for item names) - in_file: Input image' schema: type: string - name: in_file_folder in: query required: false description: 'Girder ID of parent folder for batch input image - in_file: Input image' schema: type: string - name: mag in: query required: false description: Output thumbnail magnification schema: type: number format: float - name: out_file_folder in: query required: false description: 'Girder ID of parent folder for output image - out_file: Output Region Image file' schema: type: string - name: out_file in: query required: false description: 'Name of output image - out_file: Output Region Image file' schema: type: string - name: girderApiUrl in: query required: false description: A Girder API URL (e.g., https://girder.example.com:443/api/v1) schema: type: string - name: girderToken in: query required: false description: A Girder token schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Rerun Simple Get Region tags: - slicer_cli_web /slicer_cli_web/jvizcar_braak-study_cli-tasks/hp_tau_detection/run: post: description: 'Description:

Simple Get Region

Version: 0.1.0

License: Apache 2.0

Author(s): David Gutman and Jc Vizcarra' operationId: slicer_cli_web_cliHandler_post_jvizcar_braak-study_cli-tasks_hp_tau_detection_run parameters: - name: in_file in: query required: true description: 'Girder ID of input image (if batch input, this is a regex for item names) - in_file: Input image' schema: type: string - name: in_file_folder in: query required: false description: 'Girder ID of parent folder for batch input image - in_file: Input image' schema: type: string - name: mag in: query required: true description: Output thumbnail magnification schema: type: number format: float - name: out_file_folder in: query required: true description: 'Girder ID of parent folder for output image - out_file: Output Region Image file' schema: type: string - name: out_file in: query required: true description: 'Name of output image - out_file: Output Region Image file' schema: type: string default: out_file.nrrd - name: girderApiUrl in: query required: false description: A Girder API URL (e.g., https://girder.example.com:443/api/v1) schema: type: string default: '' - name: girderToken in: query required: false description: A Girder token schema: type: string default: '' responses: '200': description: Success '400': description: A parameter was invalid. summary: Simple Get Region tags: - slicer_cli_web /slicer_cli_web/path_match: get: description: This can be very slow if name is too general. operationId: slicer_cli_web_getMatchingResource_path_match parameters: - name: name in: query required: false description: A regular expression to match the name of the resource. schema: type: string - name: path in: query required: false description: A regular expression to match the entire resource path. schema: type: string - name: relative_path in: query required: false description: A relative resource path to the base item. schema: type: string - name: base_id in: query required: false description: The base girder id for the relative path schema: type: string - name: base_type in: query required: false description: The base girder type for the relative path schema: type: string - name: type in: query required: true description: The type of the resource (item, file, etc.). schema: type: string responses: '200': description: Success '400': description: 'Invalid resource type. No matches.' summary: Get the most recently updated resource that has a name and path that matches a regular expression tags: - slicer_cli_web /system/access_flag: get: operationId: system_getAccessFlags_access_flag responses: '200': description: Success '400': description: A parameter was invalid. summary: List all access flags available in the system. tags: - system parameters: [] /system/check: get: description: Must be a system administrator to call this with any mode other than basic. operationId: system_systemStatus_check parameters: - name: mode in: query required: false description: Select details to return. "quick" are the details that can be answered without much load on the system. "slow" also includes some resource-intensive queries. schema: type: string enum: - basic - quick - slow default: basic responses: '200': description: Success '403': description: You are not a system administrator. summary: Report the current system status. tags: - system put: description: Must be a system administrator to call this. This verifies and corrects some issues, such as incorrect folder sizes. operationId: system_systemConsistencyCheck_put_check parameters: - name: progress in: query required: false description: Whether to record progress on this task. schema: type: boolean default: false responses: '200': description: Success '403': description: You are not a system administrator. summary: Perform a variety of system checks to verify that all is well. tags: - system /system/configuration: get: description: Must be a system administrator to call this. operationId: system_getConfigurationOption_configuration parameters: - name: section in: query required: true description: The section identifying the configuration option. schema: type: string - name: key in: query required: true description: The key identifying the configuration option. schema: type: string responses: '200': description: Success '403': description: You are not a system administrator. '404': description: No such option with the given section/key exists. summary: Get the value of a system configuration option. tags: - system /system/ldap_server/status: get: description: You must be an administrator to call this. operationId: system__ldapServerTest_ldap_server_status parameters: - name: uri in: query required: true description: The URI of the server. schema: type: string - name: bindName in: query required: true description: The LDAP identity to bind with. schema: type: string - name: password in: query required: true description: Password to bind with. schema: type: string responses: '200': description: Success '403': description: You are not an administrator. summary: Test connection status to a LDAP server. tags: - system /system/log: get: description: Must be a system administrator to call this. operationId: system_getLog_log parameters: - name: bytes in: query required: false description: Controls how many bytes (from the end of the log) to show. Pass 0 to show the whole log. schema: type: integer format: int32 default: 4096 - name: log in: query required: false description: Which log to tail. schema: type: string enum: - error - info default: error responses: '200': description: Success '403': description: You are not a system administrator. summary: Show the most recent contents of the server logs. tags: - system /system/log/level: get: description: Must be a system administrator to call this. operationId: system_getLogLevel_log_level responses: '200': description: Success '403': description: You are not a system administrator. summary: Get the current log level. tags: - system parameters: [] put: description: Must be a system administrator to call this. operationId: system_setLogLevel_put_log_level parameters: - name: level in: query required: true description: The new level to set. schema: type: string enum: - CRITICAL - ERROR - WARNING - INFO - DEBUG default: INFO responses: '200': description: Success '403': description: You are not a system administrator. summary: Set the current log level. tags: - system /system/plugins: get: description: Must be a system administrator to call this. operationId: system_getPlugins_plugins responses: '200': description: Success '403': description: You are not a system administrator. summary: Get the lists of all available and all loaded plugins. tags: - system parameters: [] /system/restart: put: description: Must be a system administrator to call this. operationId: system_restartServer_put_restart responses: '200': description: Success '403': description: You are not a system administrator. summary: Restart the Girder REST server. tags: - system parameters: [] /system/setting: delete: description: Must be a system administrator to call this. This is used to explicitly restore a setting to its default value. operationId: system_unsetSetting_delete_setting parameters: - name: key in: query required: true description: The key identifying the setting to unset. schema: type: string responses: '200': description: Success '403': description: You are not a system administrator. summary: Unset the value for a system setting. tags: - system get: description: Must be a system administrator to call this. operationId: system_getSetting_setting parameters: - name: key in: query required: false description: The key identifying this setting. schema: type: string - name: list in: query required: false description: A JSON list of keys representing a set of settings to return. schema: type: string responses: '200': description: Success '403': description: You are not a system administrator. summary: Get the value of a system setting, or a list of them. tags: - system put: description: Must be a system administrator to call this. If the value passed is a valid JSON object, it will be parsed and stored as an object. operationId: system_setSetting_put_setting parameters: [] responses: '200': description: Success '403': description: You are not a system administrator. '500': description: Failed to set system setting. summary: Set the value for a system setting, or a list of them. tags: - system requestBody: content: multipart/form-data: schema: type: object properties: key: type: string description: The key identifying this setting. value: type: string description: The value for this setting. list: type: string description: A JSON list of objects with key and value representing a list of settings to set. /system/setting/collection_creation_policy/access: get: description: Get result in the same structure as the access endpoints of collection, file, and group operationId: system_getCollectionCreationPolicyAccess_setting_collection_creation_policy_access responses: '200': description: Success '400': description: A parameter was invalid. summary: Get access of content creation policy. tags: - system parameters: [] /system/setting/default: get: description: Must be a system administrator to call this. operationId: system_getSettingDefault_setting_default parameters: - name: key in: query required: false description: The key identifying this setting. schema: type: string - name: list in: query required: false description: A JSON list of keys representing a set of settings to return. schema: type: string - name: default in: query required: false description: If "none", return a null value if a setting is currently the default value. If "default", return the default value of the setting(s). schema: type: string responses: '200': description: Success '403': description: You are not a system administrator. summary: Get the value of a system setting, or a list of them. tags: - system /system/uploads: delete: description: Must be a system administrator to call this. This frees resources that were allocated for the uploads and clears the uploads from database. operationId: system_discardPartialUploads_delete_uploads parameters: - name: uploadId in: query required: false description: Clear only a specific upload. schema: type: string - name: userId in: query required: false description: Restrict clearing uploads to those started by a specific user. schema: type: string - name: parentId in: query required: false description: Restrict clearing uploads to those within a specific folder or item. schema: type: string - name: assetstoreId in: query required: false description: Restrict clearing uploads within a specific assetstore. schema: type: string - name: minimumAge in: query required: false description: Restrict clearing uploads to those that are at least this many days old. schema: type: number format: float - name: includeUntracked in: query required: false description: Some assetstores can have partial uploads that are no longer in the Girder database. If this is True, remove all of them (only filtered by assetstoreId). schema: type: boolean default: true responses: '200': description: Success '403': description: You are not a system administrator. '500': description: Failed to delete upload summary: Discard uploads that have not been finished. tags: - system get: description: Must be a system administrator to call this. operationId: system_getPartialUploads_uploads parameters: - name: uploadId in: query required: false description: List only a specific upload. schema: type: string - name: userId in: query required: false description: Restrict listing uploads to those started by a specific user. schema: type: string - name: parentId in: query required: false description: Restrict listing uploads to those within a specific folder or item. schema: type: string - name: assetstoreId in: query required: false description: Restrict listing uploads within a specific assetstore. schema: type: string - name: minimumAge in: query required: false description: Restrict listing uploads to those that are at least this many days old. schema: type: number format: float - name: includeUntracked in: query required: false description: Some assetstores can have partial uploads that are no longer in the Girder database. If this is True, include all of them (only filtered by assetstoreId) in the result list. schema: type: boolean default: true - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: updated - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '403': description: You are not a system administrator. summary: Get a list of uploads that have not been finished. tags: - system /system/version: get: operationId: system_getVersion_version responses: '200': description: Success '400': description: A parameter was invalid. summary: Get the version information for this server. tags: - system parameters: [] /tcga: delete: operationId: tcga_deleteCollection_delete_tcga responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove the TCGA collection tags: - tcga parameters: [] get: operationId: tcga_getCollection_tcga responses: '200': description: Success '400': description: A parameter was invalid. summary: Get the TCGA collection tags: - tcga parameters: [] post: operationId: tcga_setCollection_post_tcga parameters: - name: collectionId in: query required: true description: The id of the collection schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Set the TCGA collection tags: - tcga /tcga/aperio: post: operationId: tcga_importTCGADocument_post_aperio parameters: - name: id in: query required: true description: The id of the item or root to import schema: type: string - name: tag in: query required: false description: Import annotations with this tag schema: type: string - name: recursive in: query required: false description: Perform a recursive search for annotations schema: type: boolean responses: '200': description: Success '400': description: A parameter was invalid. summary: Import an item as an Aperio annotation tags: - tcga /tcga/case: get: operationId: tcga_findCase_case parameters: - name: cohort in: query required: true description: The id of the cohort document schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List cases in the TCGA dataset tags: - tcga post: operationId: tcga_importCase_post_case parameters: - name: folderId in: query required: true description: The id of the folder to import schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Import a folder as a TCGA case tags: - tcga /tcga/case/label/{label}: get: operationId: tcga_getCaseByLabel_case_label_label parameters: - name: label in: path required: true description: The label of the case schema: type: string responses: '200': description: Success '400': description: Label was invalid summary: Get a case document from a label tags: - tcga /tcga/case/search: get: description: Only one of "value" or "substring" may be provided. operationId: tcga_searchCase_case_search parameters: - name: table in: query required: true description: A table to search schema: type: string - name: key in: query required: false description: A key that should be present schema: type: string - name: value in: query required: false description: The value associated with the given key schema: type: string - name: substring in: query required: false description: Find values containing this substring schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Search for cases by clinical data tags: - tcga /tcga/case/{id}: delete: operationId: tcga_deleteCase_delete_case_id parameters: - name: id in: path required: true description: The id of the case schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove a case document tags: - tcga get: operationId: tcga_getCase_case_id parameters: - name: id in: path required: true description: The id of the case schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a case document from an id tags: - tcga /tcga/case/{id}/images: get: operationId: tcga_listCaseImages_case_id_images parameters: - name: id in: path required: true description: The id of the case schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List images under a case tags: - tcga /tcga/case/{id}/metadata/tables: get: operationId: tcga_listCaseTables_case_id_metadata_tables parameters: - name: id in: path required: true description: The id of the case schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: List tables present inside case metadata tags: - tcga /tcga/case/{id}/metadata/{table}: delete: operationId: tcga_deleteCaseMetadata_delete_case_id_metadata_table parameters: - name: id in: path required: true description: The id of the case schema: type: string - name: table in: path required: true description: The table to remove schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Delete case metadata tags: - tcga get: operationId: tcga_getCaseMetadata_case_id_metadata_table parameters: - name: id in: path required: true description: The id of the case schema: type: string - name: table in: path required: true description: The table name to get schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get case metadata tags: - tcga post: operationId: tcga_setCaseMetadata_post_case_id_metadata_table parameters: - name: id in: path required: true description: The id of the case schema: type: string - name: table in: path required: true description: The table to update schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Create or replace case metadata tags: - tcga requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata to create put: description: Set metadata fields to null to delete them. operationId: tcga_updateCaseMetadata_put_case_id_metadata_table parameters: - name: id in: path required: true description: The id of the case schema: type: string - name: table in: path required: true description: The table to update schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Update case metadata tags: - tcga requestBody: content: application/json: schema: $ref: '#/components/schemas/string' required: true description: A JSON object containing the metadata to update /tcga/cohort: get: operationId: tcga_findCohort_cohort parameters: - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List cohorts in the TCGA dataset tags: - tcga post: operationId: tcga_importCohort_post_cohort parameters: - name: folderId in: query required: true description: The id of the folder to import schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Import a folder as a TCGA cohort type tags: - tcga /tcga/cohort/{id}: delete: operationId: tcga_deleteCohort_delete_cohort_id parameters: - name: id in: path required: true description: The id of the cohort schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove a cohort type tags: - tcga get: operationId: tcga_getCohort_cohort_id parameters: - name: id in: path required: true description: The id of the cohort schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a cohort document from an id tags: - tcga /tcga/cohort/{id}/images: get: operationId: tcga_cohortListImages_cohort_id_images parameters: - name: id in: path required: true description: The id of the cohort schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List slide images in a cohort tags: - tcga /tcga/cohort/{id}/slides: get: operationId: tcga_cohortListSlides_cohort_id_slides parameters: - name: id in: path required: true description: The id of the cohort schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: List slides in a cohort tags: - tcga /tcga/image: get: operationId: tcga_findImage_image parameters: - name: slide in: query required: false description: The id of slide document schema: type: string - name: caseName in: query required: false description: The name of the case schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Find images tags: - tcga post: operationId: tcga_importImage_post_image parameters: - name: itemId in: query required: true description: The id of the item to import schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Import an item as a TCGA slide image tags: - tcga /tcga/image/{id}: delete: operationId: tcga_deleteImage_delete_image_id parameters: - name: id in: path required: true description: The id of the image schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove an image tags: - tcga get: operationId: tcga_getImage_image_id parameters: - name: id in: path required: true description: The id of the image schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get an image document by id tags: - tcga /tcga/import: post: description: This will run as a local job that will execute asynchronously. operationId: tcga_importCollection_post_import responses: '200': description: Success '400': description: A parameter was invalid. summary: Recursively import the TCGA collection tags: - tcga parameters: [] /tcga/pathology: get: operationId: tcga_findPathology_pathology parameters: - name: case in: query required: true description: The id of a case document schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Find pathologies for a case tags: - tcga post: operationId: tcga_importPathology_post_pathology parameters: - name: id in: query required: true description: The id of the item to import schema: type: string - name: recursive in: query required: false description: Perform a recursive search for pathologies schema: type: boolean responses: '200': description: Success '400': description: A parameter was invalid. summary: Import an item as a TCGA pathology tags: - tcga /tcga/pathology/{id}: delete: operationId: tcga_deletePathology_delete_pathology_id parameters: - name: id in: path required: true description: The id of the pathology schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove a pathology tags: - tcga get: operationId: tcga_getPathology_pathology_id parameters: - name: id in: path required: true description: The id of the pathology schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a pathology document by id tags: - tcga /tcga/slide: get: operationId: tcga_findSlide_slide parameters: - name: case in: query required: true description: The id of case document schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: name - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success '400': description: A parameter was invalid. summary: Find slides for a case tags: - tcga post: operationId: tcga_importSlide_post_slide parameters: - name: folderId in: query required: true description: The id of the folder to import schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Import a folder as a TCGA slide tags: - tcga /tcga/slide/{id}: delete: operationId: tcga_deleteSlide_delete_slide_id parameters: - name: id in: path required: true description: The id of the slide schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Remove a slide tags: - tcga get: operationId: tcga_getSlide_slide_id parameters: - name: id in: path required: true description: The id of the slide schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. summary: Get a slide document by id tags: - tcga /token/current: get: operationId: token_currentSession_current responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Token' '400': description: A parameter was invalid. summary: Retrieve the current session information. tags: - token parameters: [] /token/scopes: get: operationId: token_listScopes_scopes responses: '200': description: Success '400': description: A parameter was invalid. summary: List all token scopes available in the system. tags: - token parameters: [] /token/session: delete: description: Attempts to delete your authentication cookie. operationId: token_deleteSession_delete_session responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Token' '400': description: A parameter was invalid. summary: Remove a session from the system. tags: - token parameters: [] get: description: If you are logged in, this will return a token associated with that login. operationId: token_getSession_session responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Token' '400': description: A parameter was invalid. summary: Get an anonymous session token for the system. tags: - token parameters: [] /user: get: operationId: user_find_user parameters: - name: text in: query required: false description: Pass this to perform a full text search for items. schema: type: string - name: limit in: query required: false description: Result set size limit. schema: type: integer format: int32 default: 50 - name: offset in: query required: false description: Offset into result set. schema: type: integer format: int32 default: 0 - name: sort in: query required: false description: Field to sort the result set by. schema: type: string default: lastName - name: sortdir in: query required: false description: 'Sort order: 1 for ascending, -1 for descending.' schema: type: integer format: int32 enum: - 1 - -1 default: 1 responses: '200': description: Success content: application/json: schema: items: $ref: '#/components/schemas/User' type: array '400': description: A parameter was invalid. summary: List or search for users. tags: - user post: operationId: user_createUser_post_user parameters: [] responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/User' '400': description: A parameter was invalid, or the specified login or email already exists in the system. summary: Create a new user. tags: - user requestBody: content: multipart/form-data: schema: type: object properties: login: type: string description: The user's requested login. email: type: string description: The user's email address. firstName: type: string description: The user's first name. lastName: type: string description: The user's last name. password: type: string format: password description: The user's requested password admin: type: boolean default: false description: Whether this user should be a site administrator. required: - login - email - firstName - lastName - password /user/authentication: delete: description: Attempts to delete your authentication cookie. operationId: user_logout_delete_authentication responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/Token' '400': description: A parameter was invalid. summary: Log out of the system. tags: - user parameters: [] get: description: Pass your username and password using HTTP Basic Auth. Sends a cookie that should be passed back in future requests. operationId: user_login_authentication parameters: - name: Girder-OTP in: header required: false description: A one-time password for this user schema: type: string responses: '200': description: Success '401': description: Missing Authorization header. '403': description: Invalid login or password. summary: Log in to the system. tags: - user /user/details: get: operationId: user_getUsersDetails_details responses: '200': description: Success '400': description: A parameter was invalid. summary: Get detailed information of accessible users. tags: - user parameters: [] /user/me: get: operationId: user_getMe_me responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/User' '400': description: A parameter was invalid. summary: Retrieve the currently logged-in user information. tags: - user parameters: [] /user/password: put: operationId: user_changePassword_put_password parameters: [] responses: '200': description: Success '400': description: Your new password is invalid. '401': description: 'You are not logged in. Your old password is incorrect.' summary: Change your password. tags: - user requestBody: content: multipart/form-data: schema: type: object properties: old: type: string format: password description: Your current password or a temporary access token. new: type: string format: password description: Your new password. required: - old - new /user/password/temporary: put: operationId: user_generateTemporaryPassword_put_password_temporary parameters: - name: email in: query required: true description: Your email address. schema: type: string responses: '200': description: Success '400': description: That email does not exist in the system. summary: Create a temporary access token for a user. The user's password is not changed. tags: - user /user/password/temporary/{id}: get: operationId: user_checkTemporaryPassword_password_temporary_id parameters: - name: id in: path required: true description: The user ID to check. schema: type: string responses: '200': description: Success '401': description: The token does not grant temporary access to the specified user. summary: Check if a specified token is a temporary access token for the specified user. If the token is valid, returns information on the token and user. tags: - user requestBody: content: multipart/form-data: schema: type: object properties: token: type: string description: The token to check. required: - token /user/verification: post: operationId: user_sendVerificationEmail_post_verification parameters: - name: login in: query required: true description: Your login or email address. schema: type: string responses: '200': description: Success '401': description: That login is not registered. summary: Send verification email. tags: - user /user/{id}: delete: operationId: user_deleteUser_delete_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: You do not have permission to delete this user. summary: Delete a user by ID. tags: - user get: operationId: user_getUser_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success content: application/json: schema: $ref: '#/components/schemas/User' '400': description: ID was invalid. '403': description: You do not have permission to see this user. summary: Get a user by ID. tags: - user put: operationId: user_updateUser_put_id parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: firstName in: query required: true description: First name of the user. schema: type: string - name: lastName in: query required: true description: Last name of the user. schema: type: string - name: email in: query required: true description: The email of the user. schema: type: string - name: admin in: query required: false description: Is the user a site admin (admin access required) schema: type: boolean - name: status in: query required: false description: The account status (admin access required) schema: type: string enum: - pending - enabled - disabled responses: '200': description: Success '400': description: A parameter was invalid. '403': description: 'You do not have write access for this user. Must be an admin to create an admin.' summary: Update a user's information. tags: - user /user/{id}/details: get: operationId: user_getUserDetails_id_details parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Read access was denied on the user. summary: Get detailed information about a user. tags: - user /user/{id}/otp: delete: operationId: user_removeOtp_delete_id_otp parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Admin access was denied on the user. summary: Disable one-time passwords for this user. tags: - user post: operationId: user_initializeOtp_post_id_otp parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Admin access was denied on the user. summary: Initiate the enablement of one-time passwords for this user. tags: - user put: operationId: user_finalizeOtp_put_id_otp parameters: - name: id in: path required: true description: The ID of the document. schema: type: string - name: Girder-OTP in: header required: true description: A one-time password for this user schema: type: string responses: '200': description: Success '400': description: A parameter was invalid. '403': description: Admin access was denied on the user. summary: Finalize the enablement of one-time passwords for this user. tags: - user /user/{id}/password: put: description: Only administrators may use this endpoint. operationId: user_changeUserPassword_put_id_password parameters: - name: id in: path required: true description: The ID of the document. schema: type: string responses: '200': description: Success '400': description: The new password is invalid. '403': description: You are not an administrator. summary: Change a user's password. tags: - user requestBody: content: multipart/form-data: schema: type: object properties: password: type: string format: password description: The user's new password. required: - password /user/{id}/quota: get: operationId: user_getUserQuota_id_quota parameters: - name: id in: path required: true description: The user ID schema: type: string responses: '200': description: Success '400': description: ID was invalid. summary: Get quota and assetstore policies for the user. tags: - user put: operationId: user_setUserQuota_put_id_quota parameters: - name: id in: path required: true description: The user ID schema: type: string - name: policy in: query required: true description: A JSON object containing the policies. This is a dictionary of keys and values. Any key that is not specified does not change. schema: type: string responses: '200': description: Success '400': description: ID was invalid. '403': description: Read permission denied on the user. summary: Set quota and assetstore policies for the user. tags: - user /user/{id}/verification: put: operationId: user_verifyEmail_put_id_verification parameters: - name: id in: path required: true description: The user ID to check. schema: type: string responses: '200': description: Success '401': description: The token is invalid or expired. summary: Verify an email address using a token. tags: - user requestBody: content: multipart/form-data: schema: type: object properties: token: type: string description: The token to check. required: - token /worker/status: get: description: Return -1 if the broker is inaccessible. operationId: worker_getWorkerStatus_status responses: '200': description: Success '400': description: A parameter was invalid. summary: Get worker status and task information. tags: - worker parameters: [] components: schemas: Annotation: type: object Assetstore: type: object Collection: type: object File: type: object Folder: type: object Group: type: object Item: type: object Token: type: object Upload: type: object User: type: object string: type: string securitySchemes: Girder-Token: in: header name: Girder-Token type: apiKey