.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
tox.ini
.github/workflows/test_and_deploy.yml
.napari/DESCRIPTION.md
examples/dataset.py
examples/generate_single_branch_skeletons.py
examples/pretrain_ssl.py
examples/pixel_embedding/download_data.py
examples/pixel_embedding/merge_point_annotations.py
examples/pixel_embedding/predict_embedding.py
examples/pixel_embedding/train_pixel_embedding_cli.py
examples/pixel_embedding/train_swin_unetr_embedding_memory_lr.py
examples/semantic_seg/train_semantic_seg.py
examples/skeletonization/split_datasets.py
examples/skeletonization/train_multiscale_skeleton.py
examples/skeletonization/train_multiscale_skeleton_lr.py
examples/skeletonization/train_semantic_multiscale_skeleton.py
examples/skeletonization/train_semantic_skeleton.py
examples/skeletonization/train_sementic_points.py
examples/skeletonization/train_skeleton.py
src/morphospaces/__init__.py
src/morphospaces/_version.py
src/morphospaces.egg-info/PKG-INFO
src/morphospaces.egg-info/SOURCES.txt
src/morphospaces.egg-info/dependency_links.txt
src/morphospaces.egg-info/entry_points.txt
src/morphospaces.egg-info/requires.txt
src/morphospaces.egg-info/top_level.txt
src/morphospaces/cli/__init__.py
src/morphospaces/cli/main.py
src/morphospaces/cli/skeletonize_cli.py
src/morphospaces/data/__init__.py
src/morphospaces/data/data_utils.py
src/morphospaces/data/skeleton.py
src/morphospaces/datasets/__init__.py
src/morphospaces/datasets/_base.py
src/morphospaces/datasets/hdf5.py
src/morphospaces/datasets/utils.py
src/morphospaces/datasets/zarr.py
src/morphospaces/datasets/_tests/__init__.py
src/morphospaces/datasets/_tests/test_hdf5.py
src/morphospaces/datasets/_tests/test_utils.py
src/morphospaces/io/__init__.py
src/morphospaces/io/hdf5.py
src/morphospaces/logging/__init__.py
src/morphospaces/logging/image.py
src/morphospaces/losses/__init__.py
src/morphospaces/losses/embedding.py
src/morphospaces/losses/regression.py
src/morphospaces/losses/segmentation.py
src/morphospaces/losses/util.py
src/morphospaces/losses/_tests/__init__.py
src/morphospaces/losses/_tests/test_embedding.py
src/morphospaces/networks/__init__.py
src/morphospaces/networks/constants.py
src/morphospaces/networks/multiscale_skeletonization.py
src/morphospaces/networks/pixel_embedding.py
src/morphospaces/networks/skeletonization.py
src/morphospaces/networks/swin_unetr.py
src/morphospaces/networks/unet.py
src/morphospaces/networks/unetr.py
src/morphospaces/networks/vit_autoencoder.py
src/morphospaces/networks/_components/__init__.py
src/morphospaces/networks/_components/embedding_swin_unetr.py
src/morphospaces/networks/_components/memory_bank.py
src/morphospaces/networks/_components/unet_blocks.py
src/morphospaces/networks/_components/unet_model.py
src/morphospaces/networks/_components/_tests/__init__.py
src/morphospaces/networks/_components/_tests/test_memory_bank.py
src/morphospaces/training/__init__.py
src/morphospaces/training/multiscale_skeletonization.py
src/morphospaces/transforms/__init__.py
src/morphospaces/transforms/image.py
src/morphospaces/transforms/label.py
src/morphospaces/transforms/skeleton.py