Index

A

angleSlice() (in module napari_dmc_brainmap.segment.processing.atlas_utils)

B

BarplotVisualization (class in napari_dmc_brainmap.visualization.vis_plots.barplot_visualization)

BrainsectionPlotter (class in napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter) BrainsectionVisualization (class in napari_dmc_brainmap.visualization.vis_plots.brainsection_visualization)

C

calculate_barplot() (in module napari_dmc_brainmap.visualization.visualization) calculate_brainsection() (in module napari_dmc_brainmap.visualization.visualization) calculate_heatmap() (in module napari_dmc_brainmap.visualization.visualization) (napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter.BrainsectionPlotter method) calculate_heatmap_difference() (napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter.BrainsectionPlotter method) calculate_plot() (napari_dmc_brainmap.visualization.vis_plots.barplot_visualization.BarplotVisualization method) (napari_dmc_brainmap.visualization.vis_plots.brainsection_visualization.BrainsectionVisualization method) (napari_dmc_brainmap.visualization.vis_plots.heatmap_visualization.HeatmapVisualization method) calculateImageGrid() (in module napari_dmc_brainmap.segment.processing.atlas_utils) CellsSegmenter (class in napari_dmc_brainmap.segment.processing.presegmentation_tools) CentroidFinder (class in napari_dmc_brainmap.segment.processing.centroid_finder) check_color_name() (napari_dmc_brainmap.utils.color_manager.ColorManager method) check_input_path() (in module napari_dmc_brainmap.utils.gui_utils) chunk_list() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools)

clean_params_dict() (in module napari_dmc_brainmap.utils.params_utils) ColorManager (class in napari_dmc_brainmap.utils.color_manager) construct_path() (in module napari_dmc_brainmap.utils.path_utils) coord_mm_transform() (in module napari_dmc_brainmap.utils.atlas_utils) count_images() (in module napari_dmc_brainmap.padding.padding) create_cells_preseg() (in module napari_dmc_brainmap.segment.segment) create_color_dict() (napari_dmc_brainmap.utils.color_manager.ColorManager method) create_color_palette() (napari_dmc_brainmap.utils.color_manager.ColorManager method) create_custom_colormap() (napari_dmc_brainmap.utils.color_manager.ColorManager method) create_directory() (in module napari_dmc_brainmap.utils.path_utils) create_dirs() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) create_general_widget() (in module napari_dmc_brainmap.preprocessing.preprocessing) create_projection_preseg() (in module napari_dmc_brainmap.segment.segment) create_regi_dict() (in module napari_dmc_brainmap.utils.general_utils)

D

DataLoader (class in napari_dmc_brainmap.utils.data_loader) do_8bit() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) do_bar_plot() (napari_dmc_brainmap.visualization.vis_plots.barplot_visualization.BarplotVisualization method) do_padding() (in module napari_dmc_brainmap.padding.padding) do_plot() (napari_dmc_brainmap.visualization.vis_plots.brainsection_visualization.BrainsectionVisualization method) (napari_dmc_brainmap.visualization.vis_plots.heatmap_visualization.HeatmapVisualization method)

do_preprocessing() (in module napari_dmc_brainmap.preprocessing.preprocessing) do_stitching() (in module napari_dmc_brainmap.stitching.stitching) downsample_and_adjust_contrast() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) downsample_image() (in module napari_dmc_brainmap.stitching.stitching_tools)

E

exclude_segment_objects() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method)

F

fill_canvas() (in module napari_dmc_brainmap.stitching.stitching_tools) find_centroids() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) find_centroids_for_image() (napari_dmc_brainmap.segment.processing.centroid_finder.CentroidFinder method)

find_common_suffix() (in module napari_dmc_brainmap.utils.path_utils) find_key_by_value() (in module napari_dmc_brainmap.utils.general_utils) fitGeoTrans() (in module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation)

G

GeneInfoDialog (class in napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog) get_ancestors() (in module napari_dmc_brainmap.visualization.vis_utils.visualization_utils) get_animal_id() (in module napari_dmc_brainmap.utils.general_utils) get_atlas_dropdown() (in module napari_dmc_brainmap.utils.dropdown_utils) get_available_atlases() (in module napari_dmc_brainmap.utils.dropdown_utils) get_bregma() (in module napari_dmc_brainmap.utils.atlas_utils) get_canvas() (in module napari_dmc_brainmap.stitching.stitching_tools) get_centroid_coord() (in module napari_dmc_brainmap.segment.segment) get_channels() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) get_cmap() (in module napari_dmc_brainmap.segment.segment) get_data_dir() (in module napari_dmc_brainmap.utils.path_utils) get_data_list() (in module napari_dmc_brainmap.utils.path_utils) get_decimal() (in module napari_dmc_brainmap.utils.atlas_utils)

get_descendants() (in module napari_dmc_brainmap.visualization.vis_utils.visualization_utils) get_drop_mask() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method) get_gene_info() (napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog.GeneInfoDialog method) get_image_list() (in module napari_dmc_brainmap.utils.path_utils) get_info() (in module napari_dmc_brainmap.utils.path_utils) get_orient_map() (in module napari_dmc_brainmap.utils.atlas_utils) get_path_to_im() (in module napari_dmc_brainmap.segment.segment) get_regi_index() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method) get_size_json() (in module napari_dmc_brainmap.stitching.stitching_tools) get_tgt_data_only() (napari_dmc_brainmap.utils.data_loader.DataLoader method) get_threshold_dropdown() (in module napari_dmc_brainmap.utils.dropdown_utils) get_unique_folder() (in module napari_dmc_brainmap.visualization.vis_utils.visualization_utils) get_xyz() (in module napari_dmc_brainmap.utils.atlas_utils)

H

HeatmapVisualization (class in napari_dmc_brainmap.visualization.vis_plots.heatmap_visualization)

I

initialize_barplot_widget() (in module napari_dmc_brainmap.visualization.visualization) initialize_brainsection_widget() (in module napari_dmc_brainmap.visualization.visualization) initialize_findcentroids_widget() (in module napari_dmc_brainmap.segment.segment) initialize_header_widget() (in module napari_dmc_brainmap.preprocessing.preprocessing) (in module napari_dmc_brainmap.visualization.visualization) initialize_heatmap_widget() (in module napari_dmc_brainmap.visualization.visualization)

initialize_loadpreseg_widget() (in module napari_dmc_brainmap.segment.segment) initialize_presegcells_widget() (in module napari_dmc_brainmap.segment.segment) initialize_presegproj_widget() (in module napari_dmc_brainmap.segment.segment) initialize_segment_widget() (in module napari_dmc_brainmap.segment.segment) initialize_widget() (in module napari_dmc_brainmap.padding.padding) (in module napari_dmc_brainmap.params.params) (in module napari_dmc_brainmap.stitching.stitching)

L

load_data() (napari_dmc_brainmap.utils.data_loader.DataLoader method) load_image() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) load_image_list() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method) load_meta() (in module napari_dmc_brainmap.stitching.stitching_tools)

load_params() (in module napari_dmc_brainmap.utils.params_utils) load_registration_data() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method) load_stitched_images() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) load_tile_stack() (in module napari_dmc_brainmap.stitching.stitching) loadAnnotBool() (in module napari_dmc_brainmap.segment.processing.atlas_utils)

M

make_binary() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) make_rgb() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) make_sharpy_track() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) make_single_channel() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) make_stack() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) map_loc() (in module napari_dmc_brainmap.stitching.stitching_tools) mapPointTransform() (in module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation) match_lists() (in module napari_dmc_brainmap.visualization.vis_utils.visualization_utils) module napari_dmc_brainmap napari_dmc_brainmap.padding napari_dmc_brainmap.padding.padding napari_dmc_brainmap.params napari_dmc_brainmap.params.params napari_dmc_brainmap.preprocessing napari_dmc_brainmap.preprocessing.preprocessing napari_dmc_brainmap.preprocessing.preprocessing_tools napari_dmc_brainmap.registration.sharpy_track napari_dmc_brainmap.registration.sharpy_track.sharpy_track napari_dmc_brainmap.registration.sharpy_track.sharpy_track.controller napari_dmc_brainmap.registration.sharpy_track.sharpy_track.images napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view napari_dmc_brainmap.results.probe_vis napari_dmc_brainmap.results.probe_vis.probe_vis napari_dmc_brainmap.results.probe_vis.probe_vis.view napari_dmc_brainmap.segment napari_dmc_brainmap.segment.processing napari_dmc_brainmap.segment.processing.atlas_utils napari_dmc_brainmap.segment.processing.centroid_finder napari_dmc_brainmap.segment.processing.presegmentation_tools napari_dmc_brainmap.segment.segment napari_dmc_brainmap.stitching napari_dmc_brainmap.stitching.stitching napari_dmc_brainmap.stitching.stitching_tools napari_dmc_brainmap.utils napari_dmc_brainmap.utils.atlas_utils napari_dmc_brainmap.utils.color_manager napari_dmc_brainmap.utils.data_loader napari_dmc_brainmap.utils.dropdown_utils napari_dmc_brainmap.utils.general_utils napari_dmc_brainmap.utils.gui_utils napari_dmc_brainmap.utils.params_utils napari_dmc_brainmap.utils.path_utils napari_dmc_brainmap.visualization napari_dmc_brainmap.visualization.vis_plots napari_dmc_brainmap.visualization.vis_plots.barplot_visualization napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter napari_dmc_brainmap.visualization.vis_plots.brainsection_visualization napari_dmc_brainmap.visualization.vis_plots.heatmap_visualization napari_dmc_brainmap.visualization.vis_utils napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog napari_dmc_brainmap.visualization.vis_utils.visualization_utils napari_dmc_brainmap.visualization.visualization

N

napari_dmc_brainmap module napari_dmc_brainmap.padding module napari_dmc_brainmap.padding.padding module napari_dmc_brainmap.params module napari_dmc_brainmap.params.params module napari_dmc_brainmap.preprocessing module napari_dmc_brainmap.preprocessing.preprocessing module napari_dmc_brainmap.preprocessing.preprocessing_tools module napari_dmc_brainmap.registration.sharpy_track module napari_dmc_brainmap.registration.sharpy_track.sharpy_track module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.controller module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.images module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view module napari_dmc_brainmap.results.probe_vis module napari_dmc_brainmap.results.probe_vis.probe_vis module napari_dmc_brainmap.results.probe_vis.probe_vis.view module napari_dmc_brainmap.segment module napari_dmc_brainmap.segment.processing module napari_dmc_brainmap.segment.processing.atlas_utils module napari_dmc_brainmap.segment.processing.centroid_finder module napari_dmc_brainmap.segment.processing.presegmentation_tools module

napari_dmc_brainmap.segment.segment module napari_dmc_brainmap.stitching module napari_dmc_brainmap.stitching.stitching module napari_dmc_brainmap.stitching.stitching_tools module napari_dmc_brainmap.utils module napari_dmc_brainmap.utils.atlas_utils module napari_dmc_brainmap.utils.color_manager module napari_dmc_brainmap.utils.data_loader module napari_dmc_brainmap.utils.dropdown_utils module napari_dmc_brainmap.utils.general_utils module napari_dmc_brainmap.utils.gui_utils module napari_dmc_brainmap.utils.params_utils module napari_dmc_brainmap.utils.path_utils module napari_dmc_brainmap.visualization module napari_dmc_brainmap.visualization.vis_plots module 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 napari_dmc_brainmap.visualization.vis_utils module napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog module napari_dmc_brainmap.visualization.vis_utils.visualization_utils module napari_dmc_brainmap.visualization.visualization module

P

padding_for_atlas() (in module napari_dmc_brainmap.stitching.stitching_tools) PaddingWidget (class in napari_dmc_brainmap.padding.padding) ParamsWidget (class in napari_dmc_brainmap.params.params) plot_brain_schematic() (napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter.BrainsectionPlotter method) plot_brain_schematic_voronoi() (napari_dmc_brainmap.visualization.vis_plots.brainsection_plotter.BrainsectionPlotter method) predictPointSample() (in module napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation) prepare_segmentation_folders() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method) preprocess_image() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) preprocess_images() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) PreprocessingWidget (class in napari_dmc_brainmap.preprocessing.preprocessing) PreSegmenter (class in napari_dmc_brainmap.segment.processing.presegmentation_tools) process_all_masks() (napari_dmc_brainmap.segment.processing.centroid_finder.CentroidFinder method) process_all_masks_parallel() (napari_dmc_brainmap.segment.processing.centroid_finder.CentroidFinder method) process_images() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) (napari_dmc_brainmap.segment.processing.presegmentation_tools.ProjectionSegmenter method)

process_images_parallel() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) (napari_dmc_brainmap.segment.processing.presegmentation_tools.ProjectionSegmenter method) process_stitch_folder() (in module napari_dmc_brainmap.stitching.stitching) process_stitch_stack() (in module napari_dmc_brainmap.stitching.stitching) progress_brainsection (napari_dmc_brainmap.visualization.visualization.VisualizationWidget attribute) progress_heatmap (napari_dmc_brainmap.visualization.visualization.VisualizationWidget attribute) progress_signal (napari_dmc_brainmap.padding.padding.PaddingWidget attribute) (napari_dmc_brainmap.preprocessing.preprocessing.PreprocessingWidget attribute) (napari_dmc_brainmap.stitching.stitching.StitchingWidget attribute) progress_signal_cells (napari_dmc_brainmap.segment.segment.SegmentWidget attribute) progress_signal_centroid (napari_dmc_brainmap.segment.segment.SegmentWidget attribute) progress_signal_projections (napari_dmc_brainmap.segment.segment.SegmentWidget attribute) ProgressBar (class in napari_dmc_brainmap.utils.gui_utils) ProjectionSegmenter (class in napari_dmc_brainmap.segment.processing.presegmentation_tools)

R

rename_image_files() (in module napari_dmc_brainmap.padding.padding)

resort_df() (in module napari_dmc_brainmap.visualization.vis_utils.visualization_utils)

S

save_image_names_csv() (in module napari_dmc_brainmap.padding.padding) save_mask_image() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) save_to_csv() (napari_dmc_brainmap.segment.processing.presegmentation_tools.PreSegmenter method) save_zstack() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools) segment_cells() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) segment_image() (napari_dmc_brainmap.segment.processing.presegmentation_tools.CellsSegmenter method) segment_projection() (napari_dmc_brainmap.segment.processing.presegmentation_tools.ProjectionSegmenter method) SegmentWidget (class in napari_dmc_brainmap.segment.segment) select_chans() (in module napari_dmc_brainmap.preprocessing.preprocessing_tools)

select_file() (napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog.GeneInfoDialog method) set_value() (napari_dmc_brainmap.utils.gui_utils.ProgressBar method) setup_ui() (napari_dmc_brainmap.visualization.vis_utils.gene_info_dialog.GeneInfoDialog method) sort_ap_dv_ml() (in module napari_dmc_brainmap.utils.atlas_utils) split_strings_layers() (in module napari_dmc_brainmap.utils.general_utils) split_to_list() (in module napari_dmc_brainmap.utils.general_utils) stitch_folder() (in module napari_dmc_brainmap.stitching.stitching_tools) stitch_stack() (in module napari_dmc_brainmap.stitching.stitching_tools) StitchingWidget (class in napari_dmc_brainmap.stitching.stitching)

U

update_params_dict() (in module napari_dmc_brainmap.utils.params_utils)

V

VisualizationWidget (class in napari_dmc_brainmap.visualization.visualization)

X

xyz_atlas_transform() (in module napari_dmc_brainmap.utils.atlas_utils)