CellProfiler Pipeline: http://www.cellprofiler.org Version:5 DateRevision:407 GitHash: ModuleCount:82 HasImagePlaneDetails:False LoadData:[module_num:1|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Input data file location:Default Input Folder sub-folder|colcc/work/d8/f51229ea8f62be33356146a4aba16b Name of the file:CRC_2-cp3_normalized_tiff_metadata.csv Load images based on this data?:Yes Base image location:None| Process just a range of rows?:No Rows to process:1,100000 Group images by metadata?:Yes Select metadata tags for grouping:sample_name Rescale intensities?:No Threshold:[module_num:2|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CAMK4 Name the output image:CP3_CAMK4_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:3|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD11c Name the output image:CP3_CD11c_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:4|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD16 Name the output image:CP3_CD16_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:5|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD20 Name the output image:CP3_CD20_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:6|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD27 Name the output image:CP3_CD27_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:7|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD3 Name the output image:CP3_CD3_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:8|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD34 Name the output image:CP3_CD34_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:9|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD4 Name the output image:CP3_CD4_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:10|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD45 Name the output image:CP3_CD45_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:11|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD45RA Name the output image:CP3_CD45RA_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:12|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD45RO Name the output image:CP3_CD45RO_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:13|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD68 Name the output image:CP3_CD68_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:14|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD8a Name the output image:CP3_CD8a_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:15|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CollagenIV Name the output image:CP3_CollagenIV_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:16|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:DNA1 Name the output image:CP3_DNA1_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:17|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:FoxP3 Name the output image:CP3_FoxP3_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:18|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:IFNA5 Name the output image:CP3_IFNA5_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:19|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:IgA Name the output image:CP3_IgA_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:20|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:IgM Name the output image:CP3_IgM_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:21|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:Ki67 Name the output image:CP3_Ki67_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:22|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:PD1 Name the output image:CP3_PD1_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:23|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:PDL1 Name the output image:CP3_PDL1_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:24|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:PanKeratin Name the output image:CP3_PanKeratin_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:25|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:SMA Name the output image:CP3_SMA_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:26|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:VEGFc Name the output image:CP3_VEGFc_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:27|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:Vimentin Name the output image:CP3_Vimentin_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu Threshold:[module_num:28|svn_version:'Unknown'|variable_revision_number:12|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:eCadherin Name the output image:CP3_eCadherin_Threshold Threshold strategy:Global Thresholding method:Robust Background Threshold smoothing scale:0.0 Threshold correction factor:1.0 Lower and upper bounds on threshold:0.6,1.0 Manual threshold:0.0 Select the measurement to threshold with:None Two-class or three-class thresholding?:Two classes Log transform before thresholding?:No Assign pixels in the middle intensity class to the foreground or the background?:Foreground Size of adaptive window:50 Lower outlier fraction:0.05 Upper outlier fraction:0.05 Averaging method:Mean Variance method:Standard deviation # of deviations:2.0 Thresholding method:Otsu MaskImage:[module_num:29|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CAMK4 Name the output image:CP3_CAMK4_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CAMK4_Threshold Invert the mask?:No MaskImage:[module_num:30|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD11c Name the output image:CP3_CD11c_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD11c_Threshold Invert the mask?:No MaskImage:[module_num:31|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD16 Name the output image:CP3_CD16_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD16_Threshold Invert the mask?:No MaskImage:[module_num:32|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD20 Name the output image:CP3_CD20_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD20_Threshold Invert the mask?:No MaskImage:[module_num:33|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD27 Name the output image:CP3_CD27_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD27_Threshold Invert the mask?:No MaskImage:[module_num:34|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD3 Name the output image:CP3_CD3_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD3_Threshold Invert the mask?:No MaskImage:[module_num:35|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD34 Name the output image:CP3_CD34_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD34_Threshold Invert the mask?:No MaskImage:[module_num:36|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD4 Name the output image:CP3_CD4_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD4_Threshold Invert the mask?:No MaskImage:[module_num:37|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD45 Name the output image:CP3_CD45_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD45_Threshold Invert the mask?:No MaskImage:[module_num:38|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD45RA Name the output image:CP3_CD45RA_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD45RA_Threshold Invert the mask?:No MaskImage:[module_num:39|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD45RO Name the output image:CP3_CD45RO_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD45RO_Threshold Invert the mask?:No MaskImage:[module_num:40|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD68 Name the output image:CP3_CD68_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD68_Threshold Invert the mask?:No MaskImage:[module_num:41|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CD8a Name the output image:CP3_CD8a_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CD8a_Threshold Invert the mask?:No MaskImage:[module_num:42|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:CollagenIV Name the output image:CP3_CollagenIV_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_CollagenIV_Threshold Invert the mask?:No MaskImage:[module_num:43|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:DNA1 Name the output image:CP3_DNA1_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_DNA1_Threshold Invert the mask?:No MaskImage:[module_num:44|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:FoxP3 Name the output image:CP3_FoxP3_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_FoxP3_Threshold Invert the mask?:No MaskImage:[module_num:45|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:IFNA5 Name the output image:CP3_IFNA5_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_IFNA5_Threshold Invert the mask?:No MaskImage:[module_num:46|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:IgA Name the output image:CP3_IgA_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_IgA_Threshold Invert the mask?:No MaskImage:[module_num:47|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:IgM Name the output image:CP3_IgM_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_IgM_Threshold Invert the mask?:No MaskImage:[module_num:48|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:Ki67 Name the output image:CP3_Ki67_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_Ki67_Threshold Invert the mask?:No MaskImage:[module_num:49|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:PD1 Name the output image:CP3_PD1_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_PD1_Threshold Invert the mask?:No MaskImage:[module_num:50|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:PDL1 Name the output image:CP3_PDL1_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_PDL1_Threshold Invert the mask?:No MaskImage:[module_num:51|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:PanKeratin Name the output image:CP3_PanKeratin_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_PanKeratin_Threshold Invert the mask?:No MaskImage:[module_num:52|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:SMA Name the output image:CP3_SMA_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_SMA_Threshold Invert the mask?:No MaskImage:[module_num:53|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:VEGFc Name the output image:CP3_VEGFc_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_VEGFc_Threshold Invert the mask?:No MaskImage:[module_num:54|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:Vimentin Name the output image:CP3_Vimentin_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_Vimentin_Threshold Invert the mask?:No MaskImage:[module_num:55|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the input image:eCadherin Name the output image:CP3_eCadherin_Masked Use objects or an image as a mask?:Image Select object for mask:None Select image for mask:CP3_eCadherin_Threshold Invert the mask?:No SaveImages:[module_num:56|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CAMK4_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CAMK4-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:57|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD11c_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD11c-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:58|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD16_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD16-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:59|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD20_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD20-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:60|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD27_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD27-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:61|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD34_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD34-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:62|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD3_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD3-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:63|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD45RA_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD45RA-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:64|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD45RO_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD45RO-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:65|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD45_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD45-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:66|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD4_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD4-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:67|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD68_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD68-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:68|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CD8a_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CD8a-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:69|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_CollagenIV_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-CollagenIV-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:70|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_DNA1_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-DNA1-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:71|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_FoxP3_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-FoxP3-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:72|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_IFNA5_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-IFNA5-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:73|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_IgA_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-IgA-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:74|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_IgM_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-IgM-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:75|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_Ki67_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-Ki67-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:76|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_PD1_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-PD1-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:77|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_PDL1_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-PDL1-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:78|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_PanKeratin_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-PanKeratin-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:79|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_SMA_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-SMA-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:80|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_VEGFc_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-VEGFc-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:81|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_Vimentin_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-Vimentin-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time) SaveImages:[module_num:82|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the type of image to save:Image Select the image to save:CP3_eCadherin_Masked Select method for constructing file names:Single name Select image name for file prefix:141Pr-SMA Enter single file name:\g-eCadherin-Preprocessed Number of digits:4 Append a suffix to the image file name?:Yes Text to append to the image name:\g Saved file format:tiff Output file location:Default Output Folder| Image bit depth:16-bit integer Overwrite existing files without warning?:Yes When to save:Every cycle Record the file and path information to the saved image?:No Create subfolders in the output folder?:No Base image folder:Elsewhere...| How to save the series:T (Time)