napari_dmc_brainmap.segment package

Subpackages

• napari_dmc_brainmap.segment.processing package
  • Submodules
  • napari_dmc_brainmap.segment.processing.atlas_utils module
    • angleSlice()
    • calculateImageGrid()
    • loadAnnotBool()
  • napari_dmc_brainmap.segment.processing.centroid_finder module
    • CentroidFinder
      • CentroidFinder.find_centroids_for_image()
      • CentroidFinder.process_all_masks()
      • CentroidFinder.process_all_masks_parallel()
  • napari_dmc_brainmap.segment.processing.presegmentation_tools module
    • CellsSegmenter
      • CellsSegmenter.find_centroids()
      • CellsSegmenter.load_image()
      • CellsSegmenter.preprocess_image()
      • CellsSegmenter.process_images()
      • CellsSegmenter.process_images_parallel()
      • CellsSegmenter.save_mask_image()
      • CellsSegmenter.segment_cells()
      • CellsSegmenter.segment_image()
    • PreSegmenter
      • PreSegmenter.exclude_segment_objects()
      • PreSegmenter.get_drop_mask()
      • PreSegmenter.get_regi_index()
      • PreSegmenter.load_image_list()
      • PreSegmenter.load_registration_data()
      • PreSegmenter.prepare_segmentation_folders()
      • PreSegmenter.save_to_csv()
    • ProjectionSegmenter
      • ProjectionSegmenter.process_images()
      • ProjectionSegmenter.process_images_parallel()
      • ProjectionSegmenter.segment_projection()
  • Module contents

Submodules

napari_dmc_brainmap.segment.segment module

class napari_dmc_brainmap.segment.segment.SegmentWidget(napari_viewer: Viewer)

Bases: QWidget

QWidget for configuring and running segmentation processes for cells and projections.

progress_signal_cells

progress_signal_centroid

progress_signal_projections

napari_dmc_brainmap.segment.segment.create_cells_preseg(cells_segmenter: CellsSegmenter, progress_signal_cells: pyqtSignal) → str

Perform pre-segmentation of cells.

Parameters:

• cells_segmenter (CellsSegmenter) – The cells segmentation instance.

• progress_signal_cells (Signal) – Progress signal for updating the progress bar.

Returns:

Status of the operation.

Return type:

str

napari_dmc_brainmap.segment.segment.create_projection_preseg(projection_segmenter: ProjectionSegmenter, progress_signal_projections: pyqtSignal) → str

Perform pre-segmentation of projections.

Parameters:

• projection_segmenter (ProjectionSegmenter) – The projections segmentation instance.

• progress_signal_projections (Signal) – Progress signal for updating the progress bar.

Returns:

Status of the operation.

Return type:

str

napari_dmc_brainmap.segment.segment.get_centroid_coord(centroid_finder: CentroidFinder, progress_signal_centroid: pyqtSignal) → str

Perform centroid finding on pre-segmented data.

Parameters:

• centroid_finder (CentroidFinder) – The centroid finder instance.

• progress_signal_centroid (Signal) – Progress signal for updating the progress bar.

Returns:

Status of the operation.

Return type:

str

napari_dmc_brainmap.segment.segment.get_cmap(name: str) → Dict[str, str]

Retrieve colormap definitions for specific segmentation types.

Parameters:

name (str) – Name of the colormap category.

Returns:

Mapping of segmentation types to colors.

Return type:

Dict[str, str]

napari_dmc_brainmap.segment.segment.get_path_to_im(input_path: Path, image_idx: int, single_channel: bool = False, chan: str | None = None, pre_seg: bool = False) → Path | str

Get the path to the image to be segmented.

Parameters:

• input_path (Path) – Path to the base input directory.

• image_idx (int) – Index of the image to retrieve.

• single_channel (bool, optional) – Whether to use single-channel images. Defaults to False.

• chan (str, optional) – The specific channel to retrieve. Defaults to None.

• pre_seg (bool, optional) – Whether to retrieve the image name for pre-segmentation. Defaults to False.

Returns:

The path to the image or the name of the image.

Return type:

Union[Path, str]

napari_dmc_brainmap.segment.segment.initialize_findcentroids_widget()

Initialize the widget for configuring centroid detection of pre-segmentation data.

Returns:

The initialized widget for centroid detection.

Return type:

FunctionGui

napari_dmc_brainmap.segment.segment.initialize_loadpreseg_widget() → FunctionGui

Initialize the widget for loading pre-segmentation data.

Returns:

The initialized widget for loading pre-segmentation data.

Return type:

FunctionGui

napari_dmc_brainmap.segment.segment.initialize_presegcells_widget()

Initialize the widget for configuring cells pre-segmentation.

Returns:

The initialized widget for cells pre-segmentation.

Return type:

FunctionGui

napari_dmc_brainmap.segment.segment.initialize_presegproj_widget()

Initialize the widget for configuring projections pre-segmentation.

Returns:

The initialized widget for projections pre-segmentation.

Return type:

FunctionGui

napari_dmc_brainmap.segment.segment.initialize_segment_widget() → FunctionGui

Initialize the segment widget for selecting input path and segmentation parameters.

Returns:

The initialized widget for segment configuration.

Return type:

FunctionGui

Module contents