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"postprocessing_context.quality_metrics.qm_params.amplitude_cutoff.amplitudes_bins_min_ratio", "description": "The minimum ratio between number of amplitudes for a unit and the number of bins. If the ratio is less than this threshold, the amplitude_cutoff for the unit is set to NaN.", "type": "int", "default": 5, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.amplitude_median.peak_sign", "description": "Sign of the peaks.", "type": "str", "default": "neg", "options": [ "neg", "pos", "both" ], "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nearest_neighbor.max_spikes", "description": "The number of spikes to use, per cluster. Note that the calculation can be very slow when this number is >20000.", "type": "int", "default": 10000, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nearest_neighbor.min_spikes", "description": "Minimum number of spikes.", "type": "int", "default": 10, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nearest_neighbor.n_neighbors", "description": "The number of neighbors to use.", "type": "int", "default": 4, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_isolation.max_spikes", "description": "The number of spikes to use, per cluster. Note that the calculation can be very slow when this number is >20000.", "type": "int", "default": 10000, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_isolation.min_spikes", "description": "Minimum number of spikes.", "type": "int", "default": 10, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_isolation.n_neighbors", "description": "The number of neighbors to use.", "type": "int", "default": 4, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_isolation.n_components", "description": "The number of PC components to use to project the snippets to.", "type": "int", "default": 10, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_isolation.radius_um", "description": "The radius, in um, that channels need to be within the peak channel to be included.", "type": "int", "default": 100, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_noise_overlap.max_spikes", "description": "The number of spikes to use, per cluster. Note that the calculation can be very slow when this number is >20000.", "type": "int", "default": 10000, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_noise_overlap.min_spikes", "description": "Minimum number of spikes.", "type": "int", "default": 10, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_noise_overlap.n_neighbors", "description": "The number of neighbors to use.", "type": "int", "default": 4, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_noise_overlap.n_components", "description": "The number of PC components to use to project the snippets to.", "type": "int", "default": 10, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.qm_params.nn_noise_overlap.radius_um", "description": "The radius, in um, that channels need to be within the peak channel to be included.", "type": "int", "default": 100, "options": null, "secret": false }, { "name": "postprocessing_context.quality_metrics.n_jobs", "description": "Number of jobs.", "type": "int", "default": 1, "options": null, "secret": false }, { "name": "postprocessing_context.duplicate_threshold", "description": "Duplicate threshold", "type": "float", "default": 0.9, "options": null, "secret": false }, { "name": "run_curation", "description": "Run curation", "type": "bool", "default": true, "options": null, "secret": false }, { "name": "curation_context.curation_query", "description": "Query to select units to keep after curation. Default is 'isi_violations_ratio < 0.5 and amplitude_cutoff < 0.1 and presence_ratio > 0.8'.", "type": "str", "default": "isi_violations_ratio < 0.5 and amplitude_cutoff < 0.1 and presence_ratio > 0.8", "options": null, "secret": false }, { "name": "run_visualization", "description": "Run visualization", "type": "bool", "default": true, "options": null, "secret": false }, { "name": "visualization_context.recording.timeseries.n_snippets_per_segment", "description": "Number of snippets per segment to visualize.", "type": "int", "default": 2, "options": null, "secret": false }, { "name": "visualization_context.recording.timeseries.snippet_duration_s", "description": "Duration of each snippet in seconds.", "type": "float", "default": 0.5, "options": null, "secret": false }, { "name": "visualization_context.recording.timeseries.skip", "description": "Skip traces visualization.", "type": "bool", "default": false, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.detection.peak_sign", "description": "Peak sign for peak detection.", "type": "str", "default": "neg", "options": [ "neg", "pos", "both" ], "secret": false }, { "name": "visualization_context.recording.drift.detection.detect_threshold", "description": "Threshold for peak detection.", "type": "float", "default": 5, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.detection.exclude_sweep_ms", "description": "Exclude sweep in ms around peak detection.", "type": "float", "default": 0.1, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.localization.ms_before", "description": "Time before peak in ms.", "type": "float", "default": 0.1, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.localization.ms_after", "description": "Time after peak in ms.", "type": "float", "default": 0.3, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.localization.radius_um", "description": "Radius in um for sparsifying waveforms before localization.", "type": "float", "default": 100, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.decimation_factor", "description": "The decimation factor for drift visualization. E.g. 30 means that 1 out of 30 spikes is plotted.", "type": "int", "default": 30, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.alpha", "description": "Alpha for scatter plot.", "type": "float", "default": 0.15, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.vmin", "description": "Min value for colormap.", "type": "float", "default": -200, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.vmax", "description": "Max value for colormap.", "type": "float", "default": 0, "options": null, "secret": false }, { "name": "visualization_context.recording.drift.cmap", "description": "Matplotlib colormap for drift visualization.", "type": "str", "default": "Greys_r", "options": null, "secret": false }, { "name": "visualization_context.recording.label", "description": "Label for the recording.", "type": "str", "default": "Recording visualization from SI pipelines", "options": null, "secret": false }, { "name": "visualization_context.sorting_summary.unit_table_properties", "description": "Comma-separated list of properties to show in the unit table.", "type": "str", "default": "default_qc", "options": null, "secret": false }, { "name": "visualization_context.sorting_summary.curation", "description": "Whether to show curation buttons.", "type": "bool", "default": true, "options": null, "secret": false }, { "name": "visualization_context.sorting_summary.label_choices", "description": "Comma-separated list of labels to choose from (if `curation=True`)", "type": "str", "default": "SUA, MUA, noise", "options": null, "secret": false }, { "name": "visualization_context.sorting_summary.label", "description": "Label for the sorting summary.", "type": "str", "default": "Sorting summary from SI pipelines", "options": null, "secret": false } ] }