.gitattributes
.gitignore
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/workflows/benchmark.yml
.github/workflows/build.yml
.github/workflows/main.yml
.github/workflows/publish-to-pypi.yml
.github/workflows/tests.yml
PyNutil/__init__.py
PyNutil/config.py
PyNutil/context.py
PyNutil/image_series.py
PyNutil/logging_utils.py
PyNutil.egg-info/PKG-INFO
PyNutil.egg-info/SOURCES.txt
PyNutil.egg-info/dependency_links.txt
PyNutil.egg-info/requires.txt
PyNutil.egg-info/top_level.txt
PyNutil/io/__init__.py
PyNutil/io/atlas_loader.py
PyNutil/io/colormap.py
PyNutil/io/file_operations.py
PyNutil/io/loaders.py
PyNutil/io/meshview_writer.py
PyNutil/io/nifti_writer.py
PyNutil/io/reconstruct_dzi.py
PyNutil/io/section_visualisation.py
PyNutil/io/volume_nifti.py
PyNutil/processing/__init__.py
PyNutil/processing/atlas_map.py
PyNutil/processing/reorientation.py
PyNutil/processing/section_volume.py
PyNutil/processing/utils.py
PyNutil/processing/adapters/__init__.py
PyNutil/processing/adapters/anchoring.py
PyNutil/processing/adapters/base.py
PyNutil/processing/adapters/damage.py
PyNutil/processing/adapters/deformation.py
PyNutil/processing/adapters/registry.py
PyNutil/processing/adapters/segmentation.py
PyNutil/processing/adapters/visualign_deformations.py
PyNutil/processing/analysis/__init__.py
PyNutil/processing/analysis/aggregator.py
PyNutil/processing/analysis/data_analysis.py
PyNutil/processing/analysis/region_counting.py
PyNutil/processing/pipeline/__init__.py
PyNutil/processing/pipeline/batch_processor.py
PyNutil/processing/pipeline/connected_components.py
PyNutil/processing/pipeline/section_processor.py
PyNutil/results/__init__.py
PyNutil/results/atlas.py
PyNutil/results/extraction.py
PyNutil/results/section.py
PyNutil/results/volume.py
benchmarks/benchmark.py
benchmarks/profile_detailed.py
demos/basic_example.py
demos/basic_example_custom_atlas.py
demos/basic_example_intensity.py
demos/brainglobe_coordinate_example.py
demos/brainglobe_registration_usage.py
demos/coordinate_example.py
demos/per_section_example.py
demos/plot_cells_in_brainrender.py
docs/assets/MeshView.mp4
docs/assets/PyNutil_fig1.png
docs/assets/Siibra.mp4
gui/Logo_PyNutil.ico
gui/Logo_PyNutil.png
gui/PyNutilGUI.py
gui/gui_smoke_test.py
gui/log_manager.py
gui/settings_manager.py
gui/ui_components.py
gui/validation.py
gui/workers.py
misc/PyNutil_test.json
misc/PyNutil_test.waln
misc/Tiling_script.py
misc/create_test_data.py
misc/download_and_pack_atlases_allen.py
misc/download_and_pack_atlases_waxholm.py
misc/implement_allen_downsampling.py
misc/make_white_images.py
misc/reformat_label_files.py
misc/reorient_allen_volume.py
misc/waln_to_json.py