napari_dmc_brainmap package

Subpackages

• napari_dmc_brainmap.padding package
  • Submodules
  • napari_dmc_brainmap.padding.padding module
    • PaddingWidget
      • PaddingWidget.progress_signal
    • count_images()
    • do_padding()
    • initialize_widget()
    • rename_image_files()
    • save_image_names_csv()
  • Module contents
• napari_dmc_brainmap.params package
  • Submodules
  • napari_dmc_brainmap.params.params module
    • ParamsWidget
    • initialize_widget()
  • Module contents
• napari_dmc_brainmap.preprocessing package
  • Submodules
  • napari_dmc_brainmap.preprocessing.preprocessing module
    • PreprocessingWidget
      • PreprocessingWidget.progress_signal
    • create_general_widget()
    • do_preprocessing()
    • initialize_header_widget()
  • napari_dmc_brainmap.preprocessing.preprocessing_tools module
    • chunk_list()
    • create_dirs()
    • do_8bit()
    • downsample_and_adjust_contrast()
    • get_channels()
    • load_stitched_images()
    • make_binary()
    • make_rgb()
    • make_sharpy_track()
    • make_single_channel()
    • make_stack()
    • preprocess_images()
    • save_zstack()
    • select_chans()
  • Module contents
• napari_dmc_brainmap.registration package
  • Subpackages
    • napari_dmc_brainmap.registration.sharpy_track package
      • Subpackages
      • Module contents
  • Submodules
  • napari_dmc_brainmap.registration.registration module
  • Module contents
• napari_dmc_brainmap.results package
  • Subpackages
    • napari_dmc_brainmap.results.probe_vis package
      • Subpackages
      • Module contents
    • napari_dmc_brainmap.results.results_helpers package
      • Submodules
      • napari_dmc_brainmap.results.results_helpers.results_creator module
      • napari_dmc_brainmap.results.results_helpers.results_quantifier module
      • napari_dmc_brainmap.results.results_helpers.slice_handle module
      • napari_dmc_brainmap.results.results_helpers.tract_calculator module
      • Module contents
  • Submodules
  • napari_dmc_brainmap.results.results module
  • Module contents
• napari_dmc_brainmap.segment package
  • Subpackages
    • napari_dmc_brainmap.segment.processing package
      • Submodules
      • napari_dmc_brainmap.segment.processing.atlas_utils module
      • napari_dmc_brainmap.segment.processing.centroid_finder module
      • napari_dmc_brainmap.segment.processing.presegmentation_tools module
      • Module contents
  • Submodules
  • napari_dmc_brainmap.segment.segment module
    • SegmentWidget
      • SegmentWidget.progress_signal_cells
      • SegmentWidget.progress_signal_centroid
      • SegmentWidget.progress_signal_projections
    • create_cells_preseg()
    • create_projection_preseg()
    • get_centroid_coord()
    • get_cmap()
    • get_path_to_im()
    • initialize_findcentroids_widget()
    • initialize_loadpreseg_widget()
    • initialize_presegcells_widget()
    • initialize_presegproj_widget()
    • initialize_segment_widget()
  • Module contents
• napari_dmc_brainmap.stitching package
  • Submodules
  • napari_dmc_brainmap.stitching.stitching module
    • StitchingWidget
      • StitchingWidget.progress_signal
    • do_stitching()
    • initialize_widget()
    • load_tile_stack()
    • process_stitch_folder()
    • process_stitch_stack()
  • napari_dmc_brainmap.stitching.stitching_tools module
    • downsample_image()
    • fill_canvas()
    • get_canvas()
    • get_size_json()
    • load_meta()
    • map_loc()
    • padding_for_atlas()
    • stitch_folder()
    • stitch_stack()
  • Module contents
• napari_dmc_brainmap.utils package
  • Submodules
  • napari_dmc_brainmap.utils.atlas_utils module
    • coord_mm_transform()
    • get_bregma()
    • get_decimal()
    • get_orient_map()
    • get_xyz()
    • sort_ap_dv_ml()
    • xyz_atlas_transform()
  • napari_dmc_brainmap.utils.color_manager module
    • ColorManager
      • ColorManager.check_color_name()
      • ColorManager.create_color_dict()
      • ColorManager.create_color_palette()
      • ColorManager.create_custom_colormap()
  • napari_dmc_brainmap.utils.data_loader module
    • DataLoader
      • DataLoader.get_tgt_data_only()
      • DataLoader.load_data()
  • napari_dmc_brainmap.utils.dropdown_utils module
    • get_atlas_dropdown()
    • get_available_atlases()
    • get_threshold_dropdown()
  • napari_dmc_brainmap.utils.general_utils module
    • create_regi_dict()
    • find_key_by_value()
    • get_animal_id()
    • split_strings_layers()
    • split_to_list()
  • napari_dmc_brainmap.utils.gui_utils module
    • ProgressBar
      • ProgressBar.set_value()
    • check_input_path()
  • napari_dmc_brainmap.utils.params_utils module
    • clean_params_dict()
    • load_params()
    • update_params_dict()
  • napari_dmc_brainmap.utils.path_utils module
    • construct_path()
    • create_directory()
    • find_common_suffix()
    • get_data_dir()
    • get_data_list()
    • get_image_list()
    • get_info()
  • Module contents
• napari_dmc_brainmap.visualization package
  • Subpackages
    • napari_dmc_brainmap.visualization.vis_plots package
      • Submodules
      • napari_dmc_brainmap.visualization.vis_plots.barplot_visualization module
      • napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter module
      • napari_dmc_brainmap.visualization.vis_plots.brainsection_visualization module
      • napari_dmc_brainmap.visualization.vis_plots.heatmap_visualization module
      • Module contents
    • napari_dmc_brainmap.visualization.vis_utils package
      • Submodules
      • napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog module
      • napari_dmc_brainmap.visualization.vis_utils.visualization_utils module
      • Module contents
  • Submodules
  • napari_dmc_brainmap.visualization.visualization module
    • VisualizationWidget
      • VisualizationWidget.progress_brainsection
      • VisualizationWidget.progress_heatmap
    • calculate_barplot()
    • calculate_brainsection()
    • calculate_heatmap()
    • initialize_barplot_widget()
    • initialize_brainsection_widget()
    • initialize_header_widget()
    • initialize_heatmap_widget()
  • Module contents

Module contents