Index

A

add_patch_to_empty_array() (in module liom_toolkit.segmentation.vseg.utils) align_annotations_to_volume() (in module liom_toolkit.registration.register)

align_brain_region_to_atlas() (in module liom_toolkit.registration.register) align_volume_to_allen() (in module liom_toolkit.registration.register) anti_aliasing (liom_toolkit.utils.io.CustomScaler attribute)

B

b (liom_toolkit.segmentation.vseg.model.VsegModel attribute)

build_template() (in module liom_toolkit.registration.templating) build_template_for_resolution() (in module liom_toolkit.registration.templating)

C

calculate_density() (in module liom_toolkit.segmentation.stats) calculate_metrics() (in module liom_toolkit.segmentation.vseg.utils) calculate_regional_density() (in module liom_toolkit.segmentation.stats) cl_dice() (in module liom_toolkit.segmentation.vseg.cldice) cl_score() (in module liom_toolkit.segmentation.vseg.cldice) clean_dir() (in module liom_toolkit.utils.utils) colour_image() (in module liom_toolkit.visualization.slice_extraction) compute_average_diameter() (in module liom_toolkit.segmentation.stats) compute_mask_area() (in module liom_toolkit.segmentation.stats) compute_slice_metrics() (in module liom_toolkit.segmentation.stats) construct_reference_space() (in module liom_toolkit.registration.utils) construct_reference_space_cache() (in module liom_toolkit.registration.utils) ConvBlock (class in liom_toolkit.segmentation.vseg.model) convert_allen_nrrd_to_ants() (in module liom_toolkit.registration.utils) convert_dask_to_ants() (in module liom_toolkit.utils.io) convert_hdf5_to_nifti() (in module liom_toolkit.utils.conversion) convert_hdf5_to_zarr() (in module liom_toolkit.utils.conversion)

convert_nifti_to_zarr() (in module liom_toolkit.utils.conversion) convert_nrrd_to_zarr() (in module liom_toolkit.utils.conversion) convert_to_png_for_saving() (in module liom_toolkit.utils.utils) create_and_write_mask() (in module liom_toolkit.utils.io) create_dir() (in module liom_toolkit.segmentation.vseg.utils) create_filter_image() (in module liom_toolkit.segmentation.stats) create_full_zarr_volume() (in module liom_toolkit.utils.conversion) create_heatmap() (in module liom_toolkit.segmentation.stats) create_images() (in module liom_toolkit.segmentation.vseg.training) create_mask_from_zarr() (in module liom_toolkit.utils.io) create_multichannel_zarr() (in module liom_toolkit.utils.conversion) create_patches() (in module liom_toolkit.segmentation.vseg.utils) create_template() (in module liom_toolkit.registration.templating) create_transformation_dict() (in module liom_toolkit.utils.io) crop_image() (in module liom_toolkit.segmentation.vseg.utils) current_scale (liom_toolkit.utils.io.CustomScaler attribute) CustomScaler (class in liom_toolkit.utils.io)

D

d4 (liom_toolkit.segmentation.vseg.model.VsegModel attribute) DaskClientManager (class in liom_toolkit.utils.dask_client) DecoderBlock (class in liom_toolkit.segmentation.vseg.model) deformably_register_volume() (in module liom_toolkit.registration.register) DiceBCELoss (class in liom_toolkit.segmentation.vseg.loss)

DiceLoss (class in liom_toolkit.segmentation.vseg.loss) do_upscale (liom_toolkit.utils.io.CustomScaler attribute) download_allen_atlas() (in module liom_toolkit.registration.utils) download_allen_template() (in module liom_toolkit.registration.utils) draw_branch_point_circles() (in module liom_toolkit.segmentation.stats)

E

e4 (liom_toolkit.segmentation.vseg.model.VsegModel attribute) EncoderBlock (class in liom_toolkit.segmentation.vseg.model) epoch_time() (in module liom_toolkit.segmentation.vseg.utils) erode_mask() (in module liom_toolkit.segmentation.plane_segmentation) estimate_tissue_mask() (in module liom_toolkit.segmentation.plane_segmentation) evaluate() (in module liom_toolkit.segmentation.vseg.training)

extract_and_save_slice_form_zarr() (in module liom_toolkit.visualization.slice_extraction) extract_and_save_slices_form_zarr() (in module liom_toolkit.visualization.slice_extraction) extract_label_slice() (in module liom_toolkit.visualization.slice_extraction) extract_single_slice_from_zarr() (in module liom_toolkit.visualization.slice_extraction) extract_slices_form_zarr() (in module liom_toolkit.visualization.slice_extraction) extract_zarr_to_png() (in module liom_toolkit.utils.io)

F

fill_holes_2d_3d() (in module liom_toolkit.segmentation.volume_segmentation) filter_image_to_region() (in module liom_toolkit.segmentation.stats) fix_even() (in module liom_toolkit.utils.utils) forward() (liom_toolkit.segmentation.vseg.loss.DiceBCELoss method) (liom_toolkit.segmentation.vseg.loss.DiceLoss method) (liom_toolkit.segmentation.vseg.model.ConvBlock method) (liom_toolkit.segmentation.vseg.model.DecoderBlock method) (liom_toolkit.segmentation.vseg.model.EncoderBlock method) (liom_toolkit.segmentation.vseg.model.VsegModel method)

frangi_filter() (in module liom_toolkit.segmentation.plane_segmentation)

G

generate_axes_dict() (in module liom_toolkit.utils.io) generate_itk_id_list_of_region() (in module liom_toolkit.segmentation.stats) generate_label_color_dict_allen() (in module liom_toolkit.utils.io) generate_label_color_dict_mask() (in module liom_toolkit.utils.io)

get_branching_point_count() (in module liom_toolkit.segmentation.stats) get_branching_points() (in module liom_toolkit.segmentation.stats) get_client() (liom_toolkit.utils.dask_client.DaskClientManager method) get_transformations_for_atlas() (in module liom_toolkit.registration.register) get_vessel_region() (in module liom_toolkit.segmentation.stats)

I

input_layer (liom_toolkit.utils.io.CustomScaler attribute)

L

li_threshold_image() (in module liom_toolkit.segmentation.plane_segmentation) liom_toolkit module liom_toolkit.registration module liom_toolkit.registration.register module liom_toolkit.registration.templating module liom_toolkit.registration.utils module liom_toolkit.segmentation module liom_toolkit.segmentation.plane_segmentation module liom_toolkit.segmentation.stats module liom_toolkit.segmentation.volume_segmentation module liom_toolkit.segmentation.vseg module liom_toolkit.segmentation.vseg.cldice module liom_toolkit.segmentation.vseg.data module liom_toolkit.segmentation.vseg.loss module liom_toolkit.segmentation.vseg.make_dataset module liom_toolkit.segmentation.vseg.model module

liom_toolkit.segmentation.vseg.predict_one module liom_toolkit.segmentation.vseg.training module liom_toolkit.segmentation.vseg.utils module liom_toolkit.segmentation.vseg.validation module liom_toolkit.utils module liom_toolkit.utils.conversion module liom_toolkit.utils.dask_client module liom_toolkit.utils.io module liom_toolkit.utils.utils module liom_toolkit.visualization module liom_toolkit.visualization.slice_extraction module load_allen_template() (in module liom_toolkit.utils.io) load_ants_image_from_node() (in module liom_toolkit.utils.io) load_hdf5() (in module liom_toolkit.utils.conversion) load_node_by_name() (in module liom_toolkit.utils.io) load_volume_for_registration() (in module liom_toolkit.registration.templating) load_zarr() (in module liom_toolkit.utils.io) load_zarr_image_from_node() (in module liom_toolkit.utils.io) load_zarr_transform_from_node() (in module liom_toolkit.utils.io)

M

make_train_val() (in module liom_toolkit.segmentation.vseg.make_dataset) mask_image() (in module liom_toolkit.segmentation.vseg.training) matplotlib_imshow() (in module liom_toolkit.segmentation.vseg.utils) module liom_toolkit liom_toolkit.registration liom_toolkit.registration.register liom_toolkit.registration.templating liom_toolkit.registration.utils liom_toolkit.segmentation liom_toolkit.segmentation.plane_segmentation liom_toolkit.segmentation.stats liom_toolkit.segmentation.volume_segmentation liom_toolkit.segmentation.vseg liom_toolkit.segmentation.vseg.cldice liom_toolkit.segmentation.vseg.data liom_toolkit.segmentation.vseg.loss liom_toolkit.segmentation.vseg.make_dataset liom_toolkit.segmentation.vseg.model liom_toolkit.segmentation.vseg.predict_one liom_toolkit.segmentation.vseg.training liom_toolkit.segmentation.vseg.utils liom_toolkit.segmentation.vseg.validation liom_toolkit.utils liom_toolkit.utils.conversion liom_toolkit.utils.dask_client liom_toolkit.utils.io liom_toolkit.utils.utils liom_toolkit.visualization liom_toolkit.visualization.slice_extraction

N

nearest() (liom_toolkit.utils.io.CustomScaler method)

numeric_filesort() (in module liom_toolkit.segmentation.vseg.utils)

O

order (liom_toolkit.utils.io.CustomScaler attribute)

original_image (liom_toolkit.utils.io.CustomScaler attribute)

P

patch() (in module liom_toolkit.segmentation.vseg.utils) PatchDataset (class in liom_toolkit.segmentation.vseg.data)

pre_register_brain() (in module liom_toolkit.registration.templating) predict_one() (in module liom_toolkit.segmentation.vseg.predict_one) process_image() (in module liom_toolkit.segmentation.vseg.utils)

R

remove_small_structures() (in module liom_toolkit.segmentation.plane_segmentation)

rigidly_register_volume() (in module liom_toolkit.registration.register)

S

sauvola_threshold_image() (in module liom_toolkit.segmentation.plane_segmentation) save_atlas_slice() (in module liom_toolkit.visualization.slice_extraction) save_atlas_to_zarr() (in module liom_toolkit.utils.io) save_label_to_zarr() (in module liom_toolkit.utils.io) save_vessel_slice() (in module liom_toolkit.visualization.slice_extraction) save_zarr() (in module liom_toolkit.utils.conversion)

seeding() (in module liom_toolkit.segmentation.vseg.utils) segment_2d_image() (in module liom_toolkit.segmentation.plane_segmentation) segment_3d_brain() (in module liom_toolkit.segmentation.volume_segmentation) set_client() (liom_toolkit.utils.dask_client.DaskClientManager method) set_physical_shape() (in module liom_toolkit.utils.io) show_diff() (in module liom_toolkit.segmentation.vseg.validation) subtract_background() (in module liom_toolkit.segmentation.plane_segmentation)

T

to_down_scale (liom_toolkit.utils.io.CustomScaler attribute) to_up_scale (liom_toolkit.utils.io.CustomScaler attribute)

train() (in module liom_toolkit.segmentation.vseg.training) train_model() (in module liom_toolkit.segmentation.vseg.training)

U

update_brain_name_list() (in module liom_toolkit.registration.templating)

V

validate_model() (in module liom_toolkit.segmentation.vseg.validation)

VsegModel (class in liom_toolkit.segmentation.vseg.model)