liom_toolkit package

Subpackages

• liom_toolkit.registration package
  • Submodules
    • liom_toolkit.registration.register module
      • align_annotations_to_volume()
      • align_brain_region_to_atlas()
      • align_volume_to_allen()
      • deformably_register_volume()
      • get_transformations_for_atlas()
      • rigidly_register_volume()
    • liom_toolkit.registration.templating module
      • build_template()
      • build_template_for_resolution()
      • create_template()
      • load_volume_for_registration()
      • pre_register_brain()
      • update_brain_name_list()
    • liom_toolkit.registration.utils module
      • construct_reference_space()
      • construct_reference_space_cache()
      • convert_allen_nrrd_to_ants()
      • download_allen_atlas()
      • download_allen_template()
  • Module contents
• liom_toolkit.segmentation package
  • Subpackages
    • liom_toolkit.segmentation.vseg package
      • Submodules
      • Module contents
  • Submodules
    • liom_toolkit.segmentation.plane_segmentation module
      • erode_mask()
      • estimate_tissue_mask()
      • frangi_filter()
      • li_threshold_image()
      • remove_small_structures()
      • sauvola_threshold_image()
      • segment_2d_image()
      • subtract_background()
    • liom_toolkit.segmentation.stats module
      • calculate_density()
      • calculate_regional_density()
      • compute_average_diameter()
      • compute_mask_area()
      • compute_slice_metrics()
      • create_filter_image()
      • create_heatmap()
      • draw_branch_point_circles()
      • filter_image_to_region()
      • generate_itk_id_list_of_region()
      • get_branching_point_count()
      • get_branching_points()
      • get_vessel_region()
    • liom_toolkit.segmentation.volume_segmentation module
      • fill_holes_2d_3d()
      • segment_3d_brain()
  • Module contents
• liom_toolkit.utils package
  • Submodules
    • liom_toolkit.utils.conversion module
      • convert_hdf5_to_nifti()
      • convert_hdf5_to_zarr()
      • convert_nifti_to_zarr()
      • convert_nrrd_to_zarr()
      • create_full_zarr_volume()
      • create_multichannel_zarr()
      • load_hdf5()
      • save_zarr()
    • liom_toolkit.utils.dask_client module
      • DaskClientManager
    • liom_toolkit.utils.io module
      • CustomScaler
      • convert_dask_to_ants()
      • create_and_write_mask()
      • create_mask_from_zarr()
      • create_transformation_dict()
      • extract_zarr_to_png()
      • generate_axes_dict()
      • generate_label_color_dict_allen()
      • generate_label_color_dict_mask()
      • load_allen_template()
      • load_ants_image_from_node()
      • load_node_by_name()
      • load_zarr()
      • load_zarr_image_from_node()
      • load_zarr_transform_from_node()
      • save_atlas_to_zarr()
      • save_label_to_zarr()
      • set_physical_shape()
    • liom_toolkit.utils.utils module
      • clean_dir()
      • convert_to_png_for_saving()
      • fix_even()
  • Module contents
• liom_toolkit.visualization package
  • Submodules
    • liom_toolkit.visualization.slice_extraction module
      • colour_image()
      • extract_and_save_slice_form_zarr()
      • extract_and_save_slices_form_zarr()
      • extract_label_slice()
      • extract_single_slice_from_zarr()
      • extract_slices_form_zarr()
      • save_atlas_slice()
      • save_vessel_slice()
  • Module contents

Module contents