.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
Pipfile
README.md
pyproject.toml
setup.cfg
tox.ini
update_version.py
vollseg
.github/workflows/deploy.yml
docs/care.md
docs/stardist.md
docs/stardist_lightning_vs_keras.md
docs/unet.md
plugins/napari-curvature/README.md
plugins/napari-curvature/pyproject.toml
plugins/napari-curvature/src/kapoorlabs_curvature_napari/__init__.py
plugins/napari-curvature/src/kapoorlabs_curvature_napari/_plot.py
plugins/napari-curvature/src/kapoorlabs_curvature_napari/_profile.py
plugins/napari-curvature/src/kapoorlabs_curvature_napari/_widget.py
plugins/napari-curvature/src/kapoorlabs_curvature_napari/napari.yaml
plugins/napari-curvature/src/kapoorlabs_curvature_napari/resources/kapoorlogo.png
plugins/napari-curvature/tests/test_smoke.py
plugins/napari-vollseg/README.md
plugins/napari-vollseg/pyproject.toml
plugins/napari-vollseg/src/kapoorlabs_vollseg_napari/__init__.py
plugins/napari-vollseg/src/kapoorlabs_vollseg_napari/_model_catalog.py
plugins/napari-vollseg/src/kapoorlabs_vollseg_napari/_runner.py
plugins/napari-vollseg/src/kapoorlabs_vollseg_napari/_widget.py
plugins/napari-vollseg/src/kapoorlabs_vollseg_napari/napari.yaml
plugins/napari-vollseg/src/kapoorlabs_vollseg_napari/resources/kapoorlogo.png
plugins/napari-vollseg/tests/test_smoke.py
scripts/README.md
scripts/clean_checkpoints.py
scripts/upload_pytorch_models_to_hf.py
scripts/analysis/plot_metrics.py
scripts/analysis/models_stardist_pytorch/metrics_all_in_one.png
scripts/analysis/models_unet_pytorch/metrics_all_in_one.png
scripts/conf/scenario_curvature_distribution.yaml
scripts/conf/scenario_generate_care.yaml
scripts/conf/scenario_generate_roi.yaml
scripts/conf/scenario_predict_care.yaml
scripts/conf/scenario_predict_combo.yaml
scripts/conf/scenario_predict_roi.yaml
scripts/conf/scenario_predict_stardist.yaml
scripts/conf/scenario_predict_unet.yaml
scripts/conf/scenario_segment.yaml
scripts/conf/scenario_train_care.yaml
scripts/conf/scenario_train_roi.yaml
scripts/conf/experiment_data_paths/care_predict.yaml
scripts/conf/experiment_data_paths/curvature_distribution.yaml
scripts/conf/experiment_data_paths/predict_combo_jeanzay.yaml
scripts/conf/experiment_data_paths/predict_default.yaml
scripts/conf/experiment_data_paths/predict_jeanzay.yaml
scripts/conf/experiment_data_paths/predict_jeanzay_maskunet.yaml
scripts/conf/experiment_data_paths/predict_jeanzay_stardist.yaml
scripts/conf/experiment_data_paths/predict_jeanzay_unet.yaml
scripts/conf/experiment_data_paths/roi_predict.yaml
scripts/conf/experiment_data_paths/testdataset.yaml
scripts/conf/model_paths/jeanzay.yaml
scripts/conf/parameters/care.yaml
scripts/conf/parameters/curvature_distribution.yaml
scripts/conf/parameters/default.yaml
scripts/conf/parameters/roi.yaml
scripts/conf/train_data_paths/care_default.yaml
scripts/conf/train_data_paths/care_jeanzay.yaml
scripts/conf/train_data_paths/roi_default.yaml
scripts/curvature_physics/curvature_distribution.py
scripts/curvature_physics/scenarios.py
scripts/legacy_segmentation_workflow/01_enhance_membrane.py
scripts/legacy_segmentation_workflow/01_membrane_segmentation_cellpose.py
scripts/legacy_segmentation_workflow/01_nuclei_segmentation.py
scripts/legacy_segmentation_workflow/01_segmentation_metrics.py
scripts/legacy_segmentation_workflow/01_vollcellpose_membrane_segmentation.py
scripts/legacy_segmentation_workflow/_upload_models_to_hf.py
scripts/legacy_segmentation_workflow/scenarios.py
scripts/model_prediction/_arch_loader.py
scripts/model_prediction/compare_segmentations.py
scripts/model_prediction/predict-care.py
scripts/model_prediction/predict-combo.py
scripts/model_prediction/predict-roi.py
scripts/model_prediction/predict-stardist.py
scripts/model_prediction/predict-unet.py
scripts/model_prediction/scenario_predict_care.py
scripts/model_prediction/scenario_predict_roi.py
scripts/model_prediction/scenarios.py
scripts/model_prediction/slurm_predict_care.sh
scripts/model_training/README.md
scripts/model_training/lightning-care.py
scripts/model_training/lightning-roi.py
scripts/model_training/lightning-stardist.py
scripts/model_training/lightning-unet.py
scripts/model_training/optimize-stardist-thresholds.py
scripts/model_training/scenario_optimize_stardist_thresholds.py
scripts/model_training/scenario_train_care.py
scripts/model_training/scenario_train_roi.py
scripts/model_training/scenario_train_stardist.py
scripts/model_training/scenario_train_unet.py
scripts/model_training/slurm_train_care.sh
scripts/model_training/slurm_train_care_jeanzay.sh
scripts/model_training/slurm_train_roi.sh
scripts/model_training/slurm_train_stardist_gwdg.sh
scripts/model_training/slurm_train_stardist_jeanzay.sh
scripts/model_training/slurm_train_unet_gwdg.sh
scripts/model_training/slurm_train_unet_jeanzay.sh
scripts/model_training/conf/scenario_optimize_stardist_thresholds.yaml
scripts/model_training/conf/scenario_train_stardist.yaml
scripts/model_training/conf/scenario_train_unet.yaml
scripts/model_training/conf/parameters/optimize_stardist_thresholds.yaml
scripts/model_training/conf/parameters/stardist_default.yaml
scripts/model_training/conf/parameters/unet_default.yaml
scripts/model_training/conf/train_data_paths/xenopus_default.yaml
scripts/model_training/conf/train_data_paths/xenopus_gwdg.yaml
scripts/model_training/conf/train_data_paths/xenopus_jeanzay.yaml
scripts/model_training/conf/train_data_paths/xenopus_jeanzay_unet.yaml
scripts/train_data_generation/README.md
scripts/train_data_generation/care_h5_visualizer.ipynb
scripts/train_data_generation/generate-care-training-data.py
scripts/train_data_generation/generate-roi-training-data.py
scripts/train_data_generation/generate-training-data.py
scripts/train_data_generation/h5_inspect.py
scripts/train_data_generation/h5_visualizer.ipynb
scripts/train_data_generation/merge_h5_datasets.py
scripts/train_data_generation/roi_h5_visualizer.ipynb
scripts/train_data_generation/scenario_generate.py
scripts/train_data_generation/scenario_generate_care.py
scripts/train_data_generation/scenario_generate_roi.py
scripts/train_data_generation/slurm_generate_care.sh
scripts/train_data_generation/slurm_generate_gwdg.sh
scripts/train_data_generation/slurm_generate_jeanzay.sh
scripts/train_data_generation/slurm_generate_roi.sh
scripts/train_data_generation/slurm_merge_h5.sh
scripts/train_data_generation/conf/scenario_generate.yaml
scripts/train_data_generation/conf/parameters/default.yaml
scripts/train_data_generation/conf/train_data_paths/xenopus_default.yaml
scripts/train_data_generation/conf/train_data_paths/xenopus_gwdg.yaml
scripts/train_data_generation/conf/train_data_paths/xenopus_jeanzay.yaml
scripts/train_data_generation/outputs/2026-05-10/11-07-28/generate-training-data.log
scripts/train_data_generation/outputs/2026-05-10/11-07-28/.hydra/config.yaml
scripts/train_data_generation/outputs/2026-05-10/11-07-28/.hydra/hydra.yaml
scripts/train_data_generation/outputs/2026-05-10/11-07-28/.hydra/overrides.yaml
scripts/train_data_generation/outputs/2026-05-10/11-25-56/generate-training-data.log
scripts/train_data_generation/outputs/2026-05-10/11-25-56/.hydra/config.yaml
scripts/train_data_generation/outputs/2026-05-10/11-25-56/.hydra/hydra.yaml
scripts/train_data_generation/outputs/2026-05-10/11-25-56/.hydra/overrides.yaml
src/kapoorlabs_vollseg/__init__.py
src/kapoorlabs_vollseg/_version.py
src/kapoorlabs_vollseg/fusion.py
src/kapoorlabs_vollseg/hub.py
src/kapoorlabs_vollseg/pretrained.py
src/kapoorlabs_vollseg/seedpool.py
src/kapoorlabs_vollseg.egg-info/PKG-INFO
src/kapoorlabs_vollseg.egg-info/SOURCES.txt
src/kapoorlabs_vollseg.egg-info/dependency_links.txt
src/kapoorlabs_vollseg.egg-info/requires.txt
src/kapoorlabs_vollseg.egg-info/top_level.txt
src/kapoorlabs_vollseg/_backbones/__init__.py
src/kapoorlabs_vollseg/_backbones/_config.py
src/kapoorlabs_vollseg/_backbones/care.py
src/kapoorlabs_vollseg/_backbones/care_keras.py
src/kapoorlabs_vollseg/_backbones/cellpose.py
src/kapoorlabs_vollseg/_backbones/maskunet.py
src/kapoorlabs_vollseg/_backbones/maskunet_keras.py
src/kapoorlabs_vollseg/_backbones/stardist.py
src/kapoorlabs_vollseg/_backbones/stardist_keras.py
src/kapoorlabs_vollseg/_backbones/unet.py
src/kapoorlabs_vollseg/_backbones/unet_keras.py
src/kapoorlabs_vollseg/_lightning/__init__.py
src/kapoorlabs_vollseg/_lightning/base_module.py
src/kapoorlabs_vollseg/_lightning/dataset.py
src/kapoorlabs_vollseg/_lightning/stitch.py
src/kapoorlabs_vollseg/_lightning/transforms.py
src/kapoorlabs_vollseg/_lightning/unet_dataset.py
src/kapoorlabs_vollseg/care_lightning/__init__.py
src/kapoorlabs_vollseg/care_lightning/base_module.py
src/kapoorlabs_vollseg/care_lightning/dataset.py
src/kapoorlabs_vollseg/care_lightning/lightning_trainer.py
src/kapoorlabs_vollseg/care_lightning/module.py
src/kapoorlabs_vollseg/care_lightning/optimizers.py
src/kapoorlabs_vollseg/care_lightning/presets.py
src/kapoorlabs_vollseg/care_lightning/pytorch_callbacks.py
src/kapoorlabs_vollseg/care_lightning/pytorch_datasets.py
src/kapoorlabs_vollseg/care_lightning/pytorch_loggers.py
src/kapoorlabs_vollseg/care_lightning/schedulers.py
src/kapoorlabs_vollseg/care_lightning/trainer.py
src/kapoorlabs_vollseg/care_lightning/transforms.py
src/kapoorlabs_vollseg/care_lightning/utils.py
src/kapoorlabs_vollseg/curvature/__init__.py
src/kapoorlabs_vollseg/curvature/api.py
src/kapoorlabs_vollseg/curvature/boundary.py
src/kapoorlabs_vollseg/curvature/distribution.py
src/kapoorlabs_vollseg/curvature/fit_2d.py
src/kapoorlabs_vollseg/curvature/fit_3d.py
src/kapoorlabs_vollseg/curvature/physics.py
src/kapoorlabs_vollseg/curvature/profile.py
src/kapoorlabs_vollseg/curvature/render.py
src/kapoorlabs_vollseg/curvature/timelapse.py
src/kapoorlabs_vollseg/curvature/tracking.py
src/kapoorlabs_vollseg/curvature/windows.py
src/kapoorlabs_vollseg/data/__init__.py
src/kapoorlabs_vollseg/data/io.py
src/kapoorlabs_vollseg/data/labels.py
src/kapoorlabs_vollseg/data/patches.py
src/kapoorlabs_vollseg/data/sequencer.py
src/kapoorlabs_vollseg/data/smart_patches_h5.py
src/kapoorlabs_vollseg/eval/__init__.py
src/kapoorlabs_vollseg/eval/matching.py
src/kapoorlabs_vollseg/eval/nms.py
src/kapoorlabs_vollseg/eval/threshold.py
src/kapoorlabs_vollseg/models/__init__.py
src/kapoorlabs_vollseg/models/care.py
src/kapoorlabs_vollseg/models/care_keras.py
src/kapoorlabs_vollseg/models/cellpose.py
src/kapoorlabs_vollseg/models/maskunet.py
src/kapoorlabs_vollseg/models/maskunet_keras.py
src/kapoorlabs_vollseg/models/stardist.py
src/kapoorlabs_vollseg/models/stardist_keras.py
src/kapoorlabs_vollseg/models/unet.py
src/kapoorlabs_vollseg/models/unet_keras.py
src/kapoorlabs_vollseg/pipelines/__init__.py
src/kapoorlabs_vollseg/pipelines/base.py
src/kapoorlabs_vollseg/pipelines/cellseg_factory.py
src/kapoorlabs_vollseg/pipelines/chunked.py
src/kapoorlabs_vollseg/pipelines/denoised.py
src/kapoorlabs_vollseg/pipelines/factory.py
src/kapoorlabs_vollseg/pipelines/nuclei_cellpose.py
src/kapoorlabs_vollseg/pipelines/roi.py
src/kapoorlabs_vollseg/pipelines/timelapse_predict.py
src/kapoorlabs_vollseg/pipelines/unet_stardist.py
src/kapoorlabs_vollseg/stardist/__init__.py
src/kapoorlabs_vollseg/stardist/dataset.py
src/kapoorlabs_vollseg/stardist/distance.py
src/kapoorlabs_vollseg/stardist/inference.py
src/kapoorlabs_vollseg/stardist/lightning_module.py
src/kapoorlabs_vollseg/stardist/losses.py
src/kapoorlabs_vollseg/stardist/model.py
src/kapoorlabs_vollseg/stardist/rays.py
src/kapoorlabs_vollseg/stardist/transforms.py
src/kapoorlabs_vollseg/train/__init__.py
src/kapoorlabs_vollseg/train/_checkpoint.py
src/kapoorlabs_vollseg/train/care.py
src/kapoorlabs_vollseg/train/care_keras.py
src/kapoorlabs_vollseg/train/cellpose.py
src/kapoorlabs_vollseg/train/maskunet.py
src/kapoorlabs_vollseg/train/stardist.py
src/kapoorlabs_vollseg/train/stardist_keras.py
src/kapoorlabs_vollseg/train/unet.py
src/kapoorlabs_vollseg/train/unet_keras.py
tests/__init__.py
tests/conftest.py
tests/test_combo_factory_shapes.py
tests/test_data_labels.py
tests/test_distance.py
tests/test_factory.py
tests/test_from_folder_config.py
tests/test_fusion.py
tests/test_hub.py
tests/test_lightning_dataset.py
tests/test_losses.py
tests/test_matching.py
tests/test_nms.py
tests/test_pipelines_base.py
tests/test_rays.py
tests/test_roi_pipeline.py
tests/test_seedpool.py
tests/test_stardist_backbone_faces.py
tests/test_stardist_optimizer_cache.py
tests/test_stardist_polyhedron.py
tests/test_stardist_transforms.py
tests/test_timelapse_predict.py
tests/test_unet_stardist_pipeline.py