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 locally available built-in and user-registered Cellpose models.
list[str]
list
str