CellColoc

Contents

  • Overview
    • Motivation
    • Core design
    • Main features
    • How do we define colocalization?
      • Occupancy computation
    • Interactive workflow
    • Where to start
    • License
    • Citation
  • Installation
    • Python environment and Python version
      • Installation on Windows with GPU support
      • Python version
    • PyPI
    • Interactive use
    • Cellpose 3
    • Development install
    • Updating CellColoc
    • Removing the CellColoc environment
    • User-scripts
    • Example datasets
    • Dependencies
  • Usage
    • Example data set
      • Licensing and attribution
    • 2D data analysis tutorial
      • Dataset used in this tutorial
      • How to use this tutorial
      • Imports and package bootstrap
      • Project settings
        • Data path
        • Channel assignment
        • Display names
        • Voxel scale
        • Cell segmentation and marker segmentation
        • Colocalization settings
        • Runtime settings
        • Whole-image versus ROI mode
      • Load the analysis channels
      • Optional: Draw ROIs interactively in napari
      • Optional: Save drawn ROIs or load an existing ROI mask
        • Whole-image mode
        • Interactive ROI mode
        • Saved ROI reuse mode
      • Run the ROI-wise segmentation and colocalization analysis
      • Visualize the result in napari
      • Optional: Refine Cellpose thresholds and inspect the updated result
      • Optional: Reanalyze manually edited label layers from napari
      • Export results
        • Understanding the exported Excel workbook
        • Understanding the roi_coloc_overview columns
          • ROI identity and object counts
          • ROI geometry
          • Cell-channel occupancy
          • Marker-channel occupancy
          • Optional third-channel occupancy
          • How to read the table in practice
      • Adapting this tutorial to your own data
    • Understanding exported results
      • Multi-channel colocalization workbook
        • Colocalization metric sheets
          • detailed_overlaps
          • cell_summary
          • roi_coloc_overview
          • ROI identity and counts
          • ROI geometry
          • Channel occupancy blocks
        • Channel object-property sheets
        • Shared identifier columns
        • 2D metrics
        • 3D metrics
        • Per-ROI morphology summary sheets
      • Single-channel workbook
        • object_summary
        • voxel_plausibility_check
        • roi_overview
    • 3D data analysis tutorial
      • Dataset used in this tutorial
      • How to use this tutorial
      • Imports and package bootstrap
      • Project settings
        • Input-file discovery and selection
        • Channel assignment and display names
        • Voxel scale
        • Cell-channel segmentation configuration
        • Marker-channel segmentation configuration
        • Colocalization settings
        • Runtime settings
        • Whole-image versus ROI mode
        • Napari result-layer selections
      • Load the analysis channels
      • Optional: Draw ROIs interactively in napari
      • Optional: Save drawn ROIs or load an existing ROI mask
      • Run the ROI-wise segmentation and colocalization analysis
      • Visualize the result in napari
      • Optionally set or update a global z-crop for subsequent refinement
      • Optionally refine results and visualize the updated result
        • Channel-selective refinement
        • Cellpose refinements
        • Postfilters
          • General postfilter selector
          • Minimum intensity threshold min_intensity
          • Local contrast threshold local_contrast
          • Bright pixel support bright_pixel_support
        • Z-cropping
      • Optionally reanalyze manually edited label layers from napari
      • Export results
      • Adapting this tutorial to your own data
    • Three-channel analysis tutorial
      • Dataset used in this tutorial
      • How to use this tutorial
      • Imports
      • Project settings
        • Input-file discovery and selection
        • Channel assignment and roles
        • Display names
        • Voxel scale
        • Three segmentation configs
        • Third-channel cell positivity switch
        • Runtime settings and ROI mode
      • Load the analysis channels
      • Optional ROI drawing and ROI reuse
      • Run the ROI-wise three-channel segmentation and colocalization analysis
      • Visualize the base result in napari
      • Optional global z-crop for refinement
      • Optionally refine all three channels and visualize the updated result
      • Optional manual reanalysis after napari edits
      • Visualize cells positive for channel 0 + channel 1
      • Visualize cells positive for channel 0 + channel 2
      • Visualize cells positive for channel 0 + channel 1 + channel 2
      • Export results
      • When to use this tutorial
    • Three-channel analysis with z-projection tutorial
      • Dataset used in this tutorial
      • How to use this tutorial
      • Imports
      • Project settings
        • Input-file discovery and selection
        • Channel assignment and display names
        • Voxel scale
        • Why z-projection is configured in the cell config
        • Segmentation configurations
        • Optional third channel
        • Third-channel positivity evaluation
        • Runtime settings and ROI mode
      • Load the analysis channels
      • Draw ROIs interactively in napari
      • Save the drawn ROIs or load an existing ROI mask
      • Run the ROI-wise three-channel segmentation and colocalization analysis
      • Visualize the base result in napari
      • Optionally refine the projected result and visualize the updated result
        • Important settings
      • Optionally reanalyze manually edited label layers from napari
      • Visualize cells positive for channel 0 + channel 1
      • Visualize cells positive for channel 0 + channel 2
      • Visualize cells positive for channel 0 + channel 1 + channel 2
      • Export results
    • Single-channel analysis tutorial
      • Dataset used in this tutorial
      • How to use this tutorial
      • Imports
      • Project settings
        • Data path
        • Single-channel assignment
        • Display names
        • Voxel scale
        • Segmentation config
        • Analysis config
        • Runtime settings
        • Whole-image versus ROI mode
      • Load the analysis channel
      • Optional: Draw ROIs interactively in napari
      • Optional: Save drawn ROIs or load an existing ROI mask
        • Whole-image mode
        • Interactive ROI mode
        • Saved ROI reuse mode
      • Run the ROI-wise single-channel segmentation and counting
      • Visualize the result in napari
      • Optional: Refine Cellpose thresholds and inspect the updated result
      • Optional: Reanalyze manually edited label layers from napari
      • Export results
      • Result table: object_summary
        • Identity and location columns
        • 2D morphology columns
        • 3D morphology columns
      • Result table: voxel_plausibility_check
      • Result table: roi_overview
        • ROI identity and size
        • Occupancy columns
        • Average morphology columns
    • Current usage topics
    • Recommended starting point
  • API Reference
    • Top-level package
      • 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
        • CellposeModelConfig.anisotropy
        • CellposeModelConfig.bright_pixel_measure
        • CellposeModelConfig.bright_pixel_min_count
        • CellposeModelConfig.bright_pixel_min_fraction
        • CellposeModelConfig.bright_pixel_threshold
        • CellposeModelConfig.cellprob_threshold
        • CellposeModelConfig.channel_axis
        • CellposeModelConfig.diameter
        • CellposeModelConfig.do_3d
        • CellposeModelConfig.flow3d_smooth
        • CellposeModelConfig.flow_threshold
        • CellposeModelConfig.local_contrast_k
        • CellposeModelConfig.local_contrast_shell_inner_radius
        • CellposeModelConfig.local_contrast_shell_outer_radius
        • CellposeModelConfig.min_intensity_measure
        • CellposeModelConfig.min_intensity_threshold
        • CellposeModelConfig.model_name_or_path
        • CellposeModelConfig.postfilters
        • CellposeModelConfig.prefilter
        • CellposeModelConfig.prefilter_median_size_xy
        • CellposeModelConfig.prefilter_median_size_z
        • CellposeModelConfig.prefilter_sigma_xy
        • CellposeModelConfig.prefilter_sigma_z
        • CellposeModelConfig.segmentation_method
        • CellposeModelConfig.threshold_apply_closing
        • CellposeModelConfig.threshold_background_sigma
        • CellposeModelConfig.threshold_min_hole_voxels
        • CellposeModelConfig.threshold_min_object_voxels
        • CellposeModelConfig.threshold_percentile
        • CellposeModelConfig.z_axis
        • CellposeModelConfig.z_crop
        • CellposeModelConfig.z_projection
      • ChannelConfig
        • ChannelConfig.cell_channel
        • ChannelConfig.marker_channel
        • ChannelConfig.optional_region_channel
        • 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
        • ColocalizationConfig.evaluate_optional_region_cell_positivity
        • ColocalizationConfig.min_cell_voxels
        • ColocalizationConfig.min_overlap_voxels
        • ColocalizationConfig.overlap_fraction_threshold
      • ColocalizationRunResult
        • ColocalizationRunResult.tables
        • ColocalizationRunResult.optional_region_masks
        • ColocalizationRunResult.analysis_z_bounds
        • ColocalizationRunResult.optional_region_refinement_context
        • ColocalizationRunResult.analysis_z_bounds
        • ColocalizationRunResult.cell_masks
        • ColocalizationRunResult.cell_refinement_context
        • ColocalizationRunResult.marker_masks
        • ColocalizationRunResult.marker_refinement_context
        • ColocalizationRunResult.optional_region_masks
        • ColocalizationRunResult.optional_region_refinement_context
        • ColocalizationRunResult.positive_cell_masks
        • ColocalizationRunResult.tables
      • 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
        • ColocalizationTables.detailed
        • ColocalizationTables.marker_properties
        • ColocalizationTables.overview
        • ColocalizationTables.roi_cell_summary
        • ColocalizationTables.roi_marker_summary
        • ColocalizationTables.roi_third_channel_summary
        • ColocalizationTables.summary
        • ColocalizationTables.third_channel_properties
      • 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
        • RuntimeConfig.crop_for_testing
        • RuntimeConfig.draw_rois
        • RuntimeConfig.image_loading_mode
        • RuntimeConfig.open_results
        • RuntimeConfig.process_rois
        • RuntimeConfig.use_gpu
      • SingleChannelAnalysisConfig
        • SingleChannelAnalysisConfig.min_object_voxels
        • SingleChannelAnalysisConfig.min_object_voxels
      • SingleChannelConfig
        • SingleChannelConfig.channel_index
        • 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
        • SingleChannelRunResult.analysis_z_bounds
        • SingleChannelRunResult.masks
        • SingleChannelRunResult.refinement_context
        • SingleChannelRunResult.tables
      • SingleChannelTables
        • SingleChannelTables.objects
        • SingleChannelTables.voxel_plausibility
        • SingleChannelTables.overview
        • SingleChannelTables.objects
        • SingleChannelTables.overview
        • SingleChannelTables.voxel_plausibility
      • 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()
    • Public API overview
      • cellcoloc.CellposeModelConfig
        • 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
          • CellposeModelConfig.__init__()
      • cellcoloc.ChannelConfig
        • ChannelConfig
          • ChannelConfig.cell_channel
          • ChannelConfig.marker_channel
          • ChannelConfig.optional_region_channel
          • ChannelConfig.__init__()
      • cellcoloc.ColocalizationConfig
        • ColocalizationConfig
          • ColocalizationConfig.min_cell_voxels
          • ColocalizationConfig.overlap_fraction_threshold
          • ColocalizationConfig.min_overlap_voxels
          • ColocalizationConfig.evaluate_optional_region_cell_positivity
          • ColocalizationConfig.__init__()
      • cellcoloc.DisplayNames
        • DisplayNames
          • DisplayNames.__init__()
      • cellcoloc.OptionalRegionSegmentationConfig
        • OptionalRegionSegmentationConfig
          • OptionalRegionSegmentationConfig.__init__()
      • cellcoloc.RuntimeConfig
        • RuntimeConfig
          • RuntimeConfig.draw_rois
          • RuntimeConfig.process_rois
          • RuntimeConfig.open_results
          • RuntimeConfig.use_gpu
          • RuntimeConfig.crop_for_testing
          • RuntimeConfig.image_loading_mode
          • RuntimeConfig.__init__()
      • cellcoloc.ResultsPaths
        • ResultsPaths
          • ResultsPaths.__init__()
      • cellcoloc.LoadedImageChannels
        • LoadedImageChannels
          • LoadedImageChannels.__init__()
      • cellcoloc.OptionalRegionSegmentationResult
        • OptionalRegionSegmentationResult
          • OptionalRegionSegmentationResult.__init__()
      • cellcoloc.ColocalizationTables
        • 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
          • ColocalizationTables.__init__()
      • cellcoloc.ColocalizationRunResult
        • ColocalizationRunResult
          • ColocalizationRunResult.tables
          • ColocalizationRunResult.optional_region_masks
          • ColocalizationRunResult.analysis_z_bounds
          • ColocalizationRunResult.optional_region_refinement_context
          • ColocalizationRunResult.__init__()
      • cellcoloc.build_results_paths
        • build_results_paths()
      • cellcoloc.load_analysis_images
        • load_analysis_images()
      • cellcoloc.save_roi_labels
        • save_roi_labels()
      • cellcoloc.load_roi_labels
        • load_roi_labels()
      • cellcoloc.try_load_roi_labels
        • try_load_roi_labels()
      • cellcoloc.export_analysis_outputs
        • export_analysis_outputs()
      • cellcoloc.analyze_existing_masks
        • analyze_existing_masks()
      • cellcoloc.prepare_loaded_images_for_analysis
        • prepare_loaded_images_for_analysis()
      • cellcoloc.prepare_runtime_environment
        • prepare_runtime_environment()
      • cellcoloc.get_runtime_cache_root
        • get_runtime_cache_root()
      • cellcoloc.create_full_image_roi_labels
        • create_full_image_roi_labels()
      • cellcoloc.rasterize_shapes_to_labelmask
        • rasterize_shapes_to_labelmask()
      • cellcoloc.create_roi_drawing_viewer
        • create_roi_drawing_viewer()
      • cellcoloc.save_roi_labels_from_shapes
        • save_roi_labels_from_shapes()
      • cellcoloc.get_bbox_2d
        • get_bbox_2d()
      • cellcoloc.get_roi_label_points
        • get_roi_label_points()
      • cellcoloc.create_cellpose_model
        • create_cellpose_model()
      • cellcoloc.create_cellpose_models_for_channels
        • create_cellpose_models_for_channels()
      • cellcoloc.evaluate_cellpose_model
        • evaluate_cellpose_model()
      • cellcoloc.relabel_with_offset
        • relabel_with_offset()
      • cellcoloc.filter_labels_by_size
        • filter_labels_by_size()
      • cellcoloc.get_cellpose_major_version
        • get_cellpose_major_version()
      • cellcoloc.get_available_cellpose_model_names
        • get_available_cellpose_model_names()
      • cellcoloc.segment_optional_region
        • segment_optional_region()
      • cellcoloc.run_roi_cellpose_colocalization
        • run_roi_cellpose_colocalization()
      • cellcoloc.refine_run_result_from_cellpose_cache
        • refine_run_result_from_cellpose_cache()
      • cellcoloc.build_positive_cell_mask
        • build_positive_cell_mask()
      • cellcoloc.extract_label_masks_from_viewer
        • extract_label_masks_from_viewer()
      • cellcoloc.show_optional_region_segmentation
        • show_optional_region_segmentation()
      • cellcoloc.show_analysis_results
        • show_analysis_results()
  • What’s New?
    • CellColoc changelog
    • πŸš€ CellColoc v0.0.5
      • ✨ Features
    • πŸš€ CellColoc v0.0.4
      • ✨ Features
      • πŸ“ƒ Changes
    • πŸš€ CellColoc v0.0.3
    • πŸš€ CellColoc v0.0.2
    • πŸš€ CellColoc v0.0.1
  • Contributing and Community Guidelines
    • How to Contribute
    • Contribution Guidelines
    • Requests for New File Formats and Reader Extensions
    • Code of Conduct
    • Where to Start?
CellColoc
  • Overview: module code

All modules for which code is available

  • cellcoloc.analysis
  • cellcoloc.config
  • cellcoloc.io
  • cellcoloc.roi
  • cellcoloc.runtime
  • cellcoloc.schemas
  • cellcoloc.segmentation
  • cellcoloc.single_channel
  • cellcoloc.visualization

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