.codecov.yml
.gitattributes
.gitignore
CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
.github/workflows/pr.yml
applications/contrastive_phenotyping/contrastive_cli/fit.yml
applications/contrastive_phenotyping/contrastive_cli/fit_slurm.sh
applications/contrastive_phenotyping/contrastive_cli/plot_embeddings.py
applications/contrastive_phenotyping/contrastive_cli/predict.yml
applications/contrastive_phenotyping/contrastive_cli/predict_slurm.sh
applications/contrastive_phenotyping/contrastive_scripts/demo_fit.py
applications/contrastive_phenotyping/contrastive_scripts/graphs_ConvNeXt_ResNet.py
applications/contrastive_phenotyping/contrastive_scripts/predict.py
applications/contrastive_phenotyping/contrastive_scripts/predict_infection_score_supervised.py
applications/contrastive_phenotyping/contrastive_scripts/profile_dataloader.py
applications/contrastive_phenotyping/contrastive_scripts/profile_dataloader.sh
applications/contrastive_phenotyping/contrastive_scripts/training_script.py
applications/infection_classification/Infection_classification_25DModel.py
applications/infection_classification/Infection_classification_2Dmodel.py
applications/infection_classification/Infection_classification_covnextModel.py
applications/infection_classification/classify_infection_25D.py
applications/infection_classification/classify_infection_2D.py
applications/infection_classification/classify_infection_covnext.py
applications/infection_classification/infection_classifier_testing.py
applications/infection_classification/predict_infection_classifier.py
applications/infection_classification/readme.md
docs/usage.md
docs/virtual_staining.md
docs/figures/2_5d_unet_dark.svg
docs/figures/2_5d_unet_light.svg
docs/figures/phase_to_nuclei_membrane.png
docs/figures/phase_to_nuclei_membrane.svg
docs/figures/svideo_1.png
docs/figures/svideo_3.png
docs/figures/svideo_5.png
docs/logo/viscy.svg
examples/configs/export_example.yml
examples/configs/fit_example.yml
examples/configs/predict_example.yml
examples/configs/preprocess_example.yml
examples/configs/test_example.yml
examples/virtual_staining/VS_model_inference/demo_vscyto2d.py
examples/virtual_staining/VS_model_inference/demo_vscyto3d.py
examples/virtual_staining/VS_model_inference/demo_vsneuromast.py
examples/virtual_staining/VS_model_inference/plot.py
examples/virtual_staining/dlmbl_exercise/README.md
examples/virtual_staining/dlmbl_exercise/exercise.ipynb
examples/virtual_staining/dlmbl_exercise/prepare-exercise.sh
examples/virtual_staining/dlmbl_exercise/setup.sh
examples/virtual_staining/dlmbl_exercise/solution.ipynb
examples/virtual_staining/dlmbl_exercise/solution.py
examples/virtual_staining/img2img_translation/README.md
examples/virtual_staining/img2img_translation/prepare-exercise.sh
examples/virtual_staining/img2img_translation/setup.sh
examples/virtual_staining/img2img_translation/solution.ipynb
examples/virtual_staining/img2img_translation/solution.py
examples/virtual_staining/phase_contrast/README.md
examples/virtual_staining/phase_contrast/prepare-exercise.sh
examples/virtual_staining/phase_contrast/setup.sh
examples/virtual_staining/phase_contrast/solution.ipynb
examples/virtual_staining/phase_contrast/solution.py
tests/__init__.py
tests/conftest.py
tests/data/__init__.py
tests/data/test_data.py
tests/evaluation/__init__.py
tests/evaluation/test_evaluation_metrics.py
tests/light/__init__.py
tests/light/test_engine.py
tests/preprocessing/__init__.py
tests/preprocessing/generate_masks_tests.py
tests/preprocessing/resize_images_tests.py
tests/preprocessing/test_pixel_ratio.py
tests/unet/__init__.py
tests/unet/test_fcmae.py
tests/unet/networks/Unet25D_tests.py
tests/unet/networks/Unet2D_tests.py
tests/unet/networks/layers/ConvBlock2D_tests.py
tests/unet/networks/layers/ConvBlock3D_tests.py
tests/utils/__init__.py
tests/utils/image_utils_tests.py
tests/utils/masks_utils_tests.py
tests/utils/mp_utils_tests.py
tests/utils/test_aux_utils.py
viscy/__init__.py
viscy/_version.py
viscy/data_organization.md
viscy/transforms.py
viscy.egg-info/PKG-INFO
viscy.egg-info/SOURCES.txt
viscy.egg-info/dependency_links.txt
viscy.egg-info/entry_points.txt
viscy.egg-info/requires.txt
viscy.egg-info/top_level.txt
viscy/cli/__init__.py
viscy/cli/cli.py
viscy/cli/contrastive_triplet.py
viscy/cli/curator_script.py
viscy/cli/metrics_script.py
viscy/cli/readme.md
viscy/data/__init__.py
viscy/data/combined.py
viscy/data/ctmc_v1.py
viscy/data/hcs.py
viscy/data/livecell.py
viscy/data/triplet.py
viscy/data/typing.py
viscy/evaluation/__init__.py
viscy/evaluation/evaluation.py
viscy/evaluation/evaluation_metrics.py
viscy/light/embedding_writer.py
viscy/light/engine.py
viscy/light/predict_writer.py
viscy/light/trainer.py
viscy/preprocessing/generate_masks.py
viscy/preprocessing/pixel_ratio.py
viscy/preprocessing/preprocessing.md
viscy/preprocessing/readme.md
viscy/representation/__init__.py
viscy/representation/contrastive.py
viscy/scripts/README.md
viscy/scripts/count_flops.py
viscy/scripts/export_from_tensorboard.py
viscy/scripts/load_ctmc_v1.py
viscy/scripts/load_livecell.py
viscy/scripts/log_feature_map.py
viscy/scripts/network_diagram.py
viscy/scripts/profiling.py
viscy/scripts/visualize_features.py
viscy/unet/__init__.py
viscy/unet/networks/Unet25D.py
viscy/unet/networks/Unet2D.py
viscy/unet/networks/__init__.py
viscy/unet/networks/fcmae.py
viscy/unet/networks/unext2.py
viscy/unet/networks/layers/ConvBlock2D.py
viscy/unet/networks/layers/ConvBlock3D.py
viscy/unet/networks/layers/__init__.py
viscy/utils/__init__.py
viscy/utils/aux_utils.py
viscy/utils/cli_utils.py
viscy/utils/image_utils.py
viscy/utils/logging.py
viscy/utils/masks.py
viscy/utils/meta_utils.py
viscy/utils/mp_utils.py
viscy/utils/normalize.py