Contents
roi_coloc_overview
detailed_overlaps
cell_summary
object_summary
voxel_plausibility_check
roi_overview
min_intensity
local_contrast
bright_pixel_support
CellposeModelConfig
CellposeModelConfig.diameter
CellposeModelConfig.model_name_or_path
CellposeModelConfig.segmentation_method
CellposeModelConfig.do_3d
CellposeModelConfig.z_axis
CellposeModelConfig.channel_axis
CellposeModelConfig.cellprob_threshold
CellposeModelConfig.flow_threshold
CellposeModelConfig.anisotropy
CellposeModelConfig.flow3d_smooth
CellposeModelConfig.prefilter
CellposeModelConfig.prefilter_sigma_xy
CellposeModelConfig.prefilter_sigma_z
CellposeModelConfig.prefilter_median_size_xy
CellposeModelConfig.prefilter_median_size_z
CellposeModelConfig.z_crop
CellposeModelConfig.z_projection
CellposeModelConfig.threshold_percentile
CellposeModelConfig.threshold_background_sigma
CellposeModelConfig.threshold_min_object_voxels
CellposeModelConfig.threshold_min_hole_voxels
CellposeModelConfig.threshold_apply_closing
CellposeModelConfig.postfilters
CellposeModelConfig.min_intensity_measure
CellposeModelConfig.min_intensity_threshold
CellposeModelConfig.local_contrast_k
CellposeModelConfig.local_contrast_shell_inner_radius
CellposeModelConfig.local_contrast_shell_outer_radius
CellposeModelConfig.bright_pixel_measure
CellposeModelConfig.bright_pixel_threshold
CellposeModelConfig.bright_pixel_min_count
CellposeModelConfig.bright_pixel_min_fraction
ChannelConfig
ChannelConfig.cell_channel
ChannelConfig.marker_channel
ChannelConfig.optional_region_channel
ColocalizationConfig
ColocalizationConfig.min_cell_voxels
ColocalizationConfig.overlap_fraction_threshold
ColocalizationConfig.min_overlap_voxels
ColocalizationConfig.evaluate_optional_region_cell_positivity
ColocalizationRunResult
ColocalizationRunResult.tables
ColocalizationRunResult.optional_region_masks
ColocalizationRunResult.analysis_z_bounds
ColocalizationRunResult.optional_region_refinement_context
ColocalizationRunResult.cell_masks
ColocalizationRunResult.cell_refinement_context
ColocalizationRunResult.marker_masks
ColocalizationRunResult.marker_refinement_context
ColocalizationRunResult.positive_cell_masks
ColocalizationTables
ColocalizationTables.detailed
ColocalizationTables.summary
ColocalizationTables.overview
ColocalizationTables.marker_properties
ColocalizationTables.third_channel_properties
ColocalizationTables.roi_cell_summary
ColocalizationTables.roi_marker_summary
ColocalizationTables.roi_third_channel_summary
DisplayNames
DisplayNames.cell
DisplayNames.marker
DisplayNames.optional_region
DisplayNames.positive_cells
LoadedImageChannels
LoadedImageChannels.analysis_z_bounds
LoadedImageChannels.cell_image
LoadedImageChannels.is_3d
LoadedImageChannels.marker_image
LoadedImageChannels.metadata
LoadedImageChannels.optional_region_image
LoadedImageChannels.paths
LoadedImageChannels.raw_shape_tzcyx
LoadedImageChannels.raw_z_size
LoadedImageChannels.source_path
LoadedImageChannels.voxel_scale_zyx
LoadedImageChannels.z_projection_method
LoadedSingleChannelImage
LoadedSingleChannelImage.analysis_z_bounds
LoadedSingleChannelImage.image
LoadedSingleChannelImage.is_3d
LoadedSingleChannelImage.metadata
LoadedSingleChannelImage.paths
LoadedSingleChannelImage.raw_shape_tzcyx
LoadedSingleChannelImage.raw_z_size
LoadedSingleChannelImage.source_path
LoadedSingleChannelImage.voxel_scale_zyx
LoadedSingleChannelImage.z_projection_method
OptionalRegionSegmentationConfig
OptionalRegionSegmentationConfig.apply_closing
OptionalRegionSegmentationConfig.background_sigma
OptionalRegionSegmentationConfig.enabled
OptionalRegionSegmentationConfig.gaussian_sigma
OptionalRegionSegmentationConfig.method
OptionalRegionSegmentationConfig.min_hole_voxels
OptionalRegionSegmentationConfig.min_object_voxels
OptionalRegionSegmentationConfig.percentile
OptionalRegionSegmentationResult
OptionalRegionSegmentationResult.corrected_image
OptionalRegionSegmentationResult.labels
OptionalRegionSegmentationResult.mask
OptionalRegionSegmentationResult.threshold
ResultsPaths
ResultsPaths.cell_mask_path
ResultsPaths.detailed_csv_path
ResultsPaths.excel_path
ResultsPaths.marker_mask_path
ResultsPaths.optional_region_mask_path
ResultsPaths.positive_cell_mask_path
ResultsPaths.results_dir
ResultsPaths.roi_mask_path
ResultsPaths.source_path
RuntimeConfig
RuntimeConfig.draw_rois
RuntimeConfig.process_rois
RuntimeConfig.open_results
RuntimeConfig.use_gpu
RuntimeConfig.crop_for_testing
RuntimeConfig.image_loading_mode
SingleChannelAnalysisConfig
SingleChannelAnalysisConfig.min_object_voxels
SingleChannelConfig
SingleChannelConfig.channel_index
SingleChannelDisplayNames
SingleChannelDisplayNames.channel
SingleChannelDisplayNames.objects
SingleChannelResultsPaths
SingleChannelResultsPaths.excel_path
SingleChannelResultsPaths.mask_path
SingleChannelResultsPaths.object_csv_path
SingleChannelResultsPaths.results_dir
SingleChannelResultsPaths.roi_mask_path
SingleChannelResultsPaths.source_path
SingleChannelRunResult
SingleChannelRunResult.masks
SingleChannelRunResult.tables
SingleChannelRunResult.analysis_z_bounds
SingleChannelRunResult.refinement_context
SingleChannelTables
SingleChannelTables.objects
SingleChannelTables.voxel_plausibility
SingleChannelTables.overview
analyze_existing_masks()
analyze_existing_single_channel_masks()
build_positive_cell_mask()
build_results_paths()
build_single_channel_results_paths()
create_cellpose_model()
create_cellpose_models_for_channels()
create_full_image_roi_labels()
create_roi_drawing_viewer()
create_single_channel_roi_drawing_viewer()
evaluate_cellpose_model()
export_analysis_outputs()
export_single_channel_outputs()
extract_label_masks_from_viewer()
extract_single_channel_masks_from_viewer()
filter_labels_by_size()
get_available_cellpose_model_names()
get_bbox_2d()
get_cellpose_major_version()
get_roi_label_points()
get_runtime_cache_root()
load_analysis_images()
load_roi_labels()
load_single_channel_image()
prepare_loaded_images_for_analysis()
prepare_loaded_single_channel_image_for_analysis()
prepare_runtime_environment()
rasterize_shapes_to_labelmask()
refine_run_result_from_cellpose_cache()
refine_single_channel_run_result_from_cellpose_cache()
relabel_with_offset()
run_roi_cellpose_colocalization()
run_roi_single_channel_segmentation()
save_roi_labels()
save_roi_labels_from_shapes()
segment_optional_region()
show_analysis_results()
show_optional_region_segmentation()
show_single_channel_results()
try_load_roi_labels()
try_load_single_channel_roi_labels()
CellposeModelConfig.__init__()
ChannelConfig.__init__()
ColocalizationConfig.__init__()
DisplayNames.__init__()
OptionalRegionSegmentationConfig.__init__()
RuntimeConfig.__init__()
ResultsPaths.__init__()
LoadedImageChannels.__init__()
OptionalRegionSegmentationResult.__init__()
ColocalizationTables.__init__()
ColocalizationRunResult.__init__()
Return the temporary fallback directory used for runtime caches.
The directory itself is only used when one of the default library cache or config locations turns out to be unavailable for writing.
Path