.flake8
.gitignore
.readthedocs.yaml
LICENSE
README.md
env.yml
pyproject.toml
.github/workflows/deploy.yml
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
docs/requirements.txt
docs/_modules/cryovit.config.rst
docs/_modules/cryovit.datamodules.rst
docs/_modules/cryovit.datasets.rst
docs/_modules/cryovit.models.rst
docs/_modules/cryovit.run.rst
docs/_modules/cryovit.types.rst
docs/_modules/cryovit.utils.rst
docs/_static/custom.css
docs/_static/figures/label_regions.png
docs/_static/napari/dataset.png
docs/_static/napari/file_open.png
docs/_static/napari/infer.png
docs/_static/napari/infer_labels.png
docs/_static/napari/labels.png
docs/_static/napari/train.png
docs/_static/tutorial/cryovit_cli_evaluate_output.png
docs/_static/tutorial/cryovit_cli_features_output.png
docs/_static/tutorial/cryovit_cli_infer_output.png
docs/_static/tutorial/cryovit_cli_output.png
docs/_static/tutorial/cryovit_cli_train_output.png
docs/_static/tutorial/tutorial_chimerax.png
docs/development/debugging.rst
docs/napari/installation.rst
docs/napari/plugin.rst
docs/usage/commands.rst
docs/usage/dataset.rst
docs/usage/installation.rst
docs/usage/quickstart.rst
slurm_scripts/dino_features.sh
slurm_scripts/dino_features_job.sh
slurm_scripts/fractional_experiment.sh
slurm_scripts/fractional_experiment_job.sh
slurm_scripts/fractional_sample.sh
slurm_scripts/fractional_sample_job.sh
slurm_scripts/multi_experiment.sh
slurm_scripts/multi_experiment_job.sh
slurm_scripts/single_experiment.sh
slurm_scripts/single_experiment_job.sh
slurm_scripts/single_sample.sh
slurm_scripts/single_sample_job.sh
src/cryovit/__init__.py
src/cryovit/_logging_config.py
src/cryovit/_version.py
src/cryovit/config.py
src/cryovit/types.py
src/cryovit/utils.py
src/cryovit.egg-info/PKG-INFO
src/cryovit.egg-info/SOURCES.txt
src/cryovit.egg-info/dependency_links.txt
src/cryovit.egg-info/entry_points.txt
src/cryovit.egg-info/requires.txt
src/cryovit.egg-info/top_level.txt
src/cryovit/cli/__init__.py
src/cryovit/cli/cli.py
src/cryovit/cli/dino_cli.py
src/cryovit/cli/eval_cli.py
src/cryovit/cli/infer_cli.py
src/cryovit/cli/train_cli.py
src/cryovit/configs/dino_features.yaml
src/cryovit/configs/eval_model.yaml
src/cryovit/configs/infer_model.yaml
src/cryovit/configs/train_model.yaml
src/cryovit/configs/callbacks/csv_writer.yaml
src/cryovit/configs/callbacks/rich_progress_bar.yaml
src/cryovit/configs/callbacks/stochastic_weight_average.yaml
src/cryovit/configs/callbacks/test_pred_writer.yaml
src/cryovit/configs/datamodule/dino.yaml
src/cryovit/configs/datamodule/file.yaml
src/cryovit/configs/datamodule/fractional.yaml
src/cryovit/configs/datamodule/fractional_loo.yaml
src/cryovit/configs/datamodule/multi.yaml
src/cryovit/configs/datamodule/single.yaml
src/cryovit/configs/datamodule/dataloader/default.yaml
src/cryovit/configs/datamodule/dataset/file.yaml
src/cryovit/configs/datamodule/dataset/tomo.yaml
src/cryovit/configs/datamodule/dataset/vit.yaml
src/cryovit/configs/experiments/fibro_cancer_to_neuron_mito.yaml
src/cryovit/configs/experiments/fractional_bacteria.yaml
src/cryovit/configs/experiments/fractional_cristae.yaml
src/cryovit/configs/experiments/fractional_granule.yaml
src/cryovit/configs/experiments/fractional_microtubule.yaml
src/cryovit/configs/experiments/fractional_mito.yaml
src/cryovit/configs/experiments/hd_to_healthy_mito.yaml
src/cryovit/configs/experiments/healthy_to_hd_mito.yaml
src/cryovit/configs/experiments/multi_bacteria.yaml
src/cryovit/configs/experiments/multi_cristae.yaml
src/cryovit/configs/experiments/multi_granule.yaml
src/cryovit/configs/experiments/multi_microtubule.yaml
src/cryovit/configs/experiments/multi_mito.yaml
src/cryovit/configs/experiments/neuron_to_fibro_cancer_mito.yaml
src/cryovit/configs/experiments/old_to_young_mito.yaml
src/cryovit/configs/experiments/sam2_hparams.yaml
src/cryovit/configs/experiments/single_ad_mito.yaml
src/cryovit/configs/experiments/single_algae_mito.yaml
src/cryovit/configs/experiments/single_hd_dense_mito.yaml
src/cryovit/configs/experiments/single_hd_mito.yaml
src/cryovit/configs/experiments/single_membrane.yaml
src/cryovit/configs/experiments/single_rgc_mito.yaml
src/cryovit/configs/experiments/test_experiment.yaml
src/cryovit/configs/experiments/young_to_old_mito.yaml
src/cryovit/configs/hydra/hydra_logging/rich_logger.yaml
src/cryovit/configs/hydra/job_logging/rich_logger.yaml
src/cryovit/configs/logger/wandb.yaml
src/cryovit/configs/model/cryovit.yaml
src/cryovit/configs/model/default.yaml
src/cryovit/configs/model/default_sam.yaml
src/cryovit/configs/model/medsam.yaml
src/cryovit/configs/model/sam2.yaml
src/cryovit/configs/model/unet3d.yaml
src/cryovit/configs/model/losses/dice_loss.yaml
src/cryovit/configs/model/losses/focal_loss.yaml
src/cryovit/configs/model/metrics/dice_metric.yaml
src/cryovit/configs/model/metrics/f1_metric.yaml
src/cryovit/configs/paths/default.yaml
src/cryovit/configs/trainer/eval.yaml
src/cryovit/configs/trainer/fit.yaml
src/cryovit/datamodules/__init__.py
src/cryovit/datamodules/base_datamodule.py
src/cryovit/datamodules/file_datamodule.py
src/cryovit/datamodules/fractional_datamodule.py
src/cryovit/datamodules/fractional_sample_datamodule.py
src/cryovit/datamodules/multi_sample_datamodule.py
src/cryovit/datamodules/single_sample_datamodule.py
src/cryovit/datamodules/utils.py
src/cryovit/datasets/__init__.py
src/cryovit/datasets/file_dataset.py
src/cryovit/datasets/tomo_dataset.py
src/cryovit/datasets/vit_dataset.py
src/cryovit/models/__init__.py
src/cryovit/models/base_model.py
src/cryovit/models/callbacks.py
src/cryovit/models/cryovit.py
src/cryovit/models/losses.py
src/cryovit/models/metrics.py
src/cryovit/models/sam2.py
src/cryovit/models/sam2_blocks.py
src/cryovit/models/unet3d.py
src/cryovit/run/__init__.py
src/cryovit/run/dino_features.py
src/cryovit/run/eval_model.py
src/cryovit/run/infer_model.py
src/cryovit/run/train_model.py
src/cryovit/training/__init__.py
src/cryovit/training/dino_features.py
src/cryovit/training/eval_model.py
src/cryovit/training/train_model.py
src/cryovit/training/visualize_results.py
src/cryovit/visualization/__init__.py
src/cryovit/visualization/dino_pca.py
src/cryovit/visualization/fractional_sample.py
src/cryovit/visualization/multi_label_sample.py
src/cryovit/visualization/multi_sample.py
src/cryovit/visualization/segmentations.py
src/cryovit/visualization/single_sample.py
src/cryovit/visualization/sparse_sample.py
src/cryovit/visualization/utils.py