.codecov.yml
.gitattributes
.gitignore
CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
.github/workflows/pr.yml
applications/contrastive_phenotyping/contrastive_cli/fit_ctc_mps.yml
applications/contrastive_phenotyping/contrastive_cli/predict_ctc_mps.yml
applications/contrastive_phenotyping/evaluation/ALFI_displacement.py
applications/contrastive_phenotyping/evaluation/PC_vs_CF.py
applications/contrastive_phenotyping/evaluation/PC_vs_CF_singleChannel.py
applications/contrastive_phenotyping/evaluation/analyze_embeddings.py
applications/contrastive_phenotyping/evaluation/cosine_dissimilarity_dataset.py
applications/contrastive_phenotyping/evaluation/cosine_similarity.py
applications/contrastive_phenotyping/evaluation/displacement.py
applications/contrastive_phenotyping/evaluation/figure.mplstyle
applications/contrastive_phenotyping/evaluation/grad_attr.py
applications/contrastive_phenotyping/evaluation/imagenet_pretrained_features.py
applications/contrastive_phenotyping/evaluation/linear_probing.py
applications/contrastive_phenotyping/evaluation/log_regresssion_training.py
applications/contrastive_phenotyping/evaluation/pca_umap_embeddings_time.py
applications/contrastive_phenotyping/evaluation/plot_embeddings.py
applications/contrastive_phenotyping/evaluation/predict_infection_score_supervised.py
applications/contrastive_phenotyping/evaluation/time_decay_knn.py
applications/contrastive_phenotyping/examples_cli/fit.yml
applications/contrastive_phenotyping/examples_cli/fit_slurm.sh
applications/contrastive_phenotyping/examples_cli/predict.yml
applications/contrastive_phenotyping/examples_cli/predict_slurm.sh
applications/contrastive_phenotyping/figures/cell_division.py
applications/contrastive_phenotyping/figures/classify_feb.py
applications/contrastive_phenotyping/figures/classify_feb_embeddings.py
applications/contrastive_phenotyping/figures/classify_june.py
applications/contrastive_phenotyping/figures/figure_4a_1.py
applications/contrastive_phenotyping/figures/figure_4e_2_feb.py
applications/contrastive_phenotyping/figures/figure_4e_2_june.py
applications/contrastive_phenotyping/figures/figure_cell_infection.py
applications/contrastive_phenotyping/figures/organelle_dynamics.py
applications/contrastive_phenotyping/figures/save_patches.py
applications/contrastive_phenotyping/figures/track_smoothness.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/Infection_classifier_accuracy.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/dynaCLR_schematic.png
docs/figures/phase_to_nuclei_membrane.png
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docs/figures/svideo_1.png
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docs/figures/svideo_5.png
docs/figures/vs_hf_demo.gif
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/gradio/demo_gradio.py
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/preprocessing/__init__.py
tests/preprocessing/generate_masks_tests.py
tests/preprocessing/resize_images_tests.py
tests/preprocessing/test_pixel_ratio.py
tests/representation/test_lca.py
tests/translation/__init__.py
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tests/translation/test_evaluation.py
tests/translation/test_predict_writer.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
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viscy/__init__.py
viscy/_version.py
viscy/cli.py
viscy/data_organization.md
viscy/trainer.py
viscy.egg-info/PKG-INFO
viscy.egg-info/SOURCES.txt
viscy.egg-info/dependency_links.txt
viscy.egg-info/entry_points.txt
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viscy.egg-info/top_level.txt
viscy/data/__init__.py
viscy/data/combined.py
viscy/data/ctmc_v1.py
viscy/data/distributed.py
viscy/data/gpu_aug.py
viscy/data/hcs.py
viscy/data/livecell.py
viscy/data/mmap_cache.py
viscy/data/segmentation.py
viscy/data/triplet.py
viscy/data/typing.py
viscy/preprocessing/generate_masks.py
viscy/preprocessing/pixel_ratio.py
viscy/preprocessing/precompute.py
viscy/preprocessing/preprocessing.md
viscy/preprocessing/readme.md
viscy/representation/contrastive.py
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viscy/representation/engine.py
viscy/representation/evaluation/__init__.py
viscy/representation/evaluation/clustering.py
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viscy/representation/evaluation/feature.py
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viscy/scripts/README.md
viscy/scripts/bench_augmentations.py
viscy/scripts/count_flops.py
viscy/scripts/curator_script.py
viscy/scripts/effective_receptive_field.py
viscy/scripts/export_from_tensorboard.py
viscy/scripts/fit_demo_contrastive.py
viscy/scripts/graphs_ConvNeXt_ResNet.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/profile_dataloader.py
viscy/scripts/profile_dataloader.sh
viscy/scripts/profiling.py
viscy/scripts/recompute_phate.py
viscy/scripts/shared_dict.py
viscy/scripts/visualize_features.py
viscy/transforms/__init__.py
viscy/transforms/_gaussian_blur.py
viscy/transforms/_redef.py
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viscy/unet/__init__.py
viscy/unet/networks/Unet25D.py
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viscy/unet/networks/__init__.py
viscy/unet/networks/fcmae.py
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viscy/utils/mp_utils.py
viscy/utils/normalize.py