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.gitattributes
.gitignore
CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
.github/workflows/pr.yml
applications/benchmarking/DynaCLR/ImageNet/config.yml
applications/benchmarking/DynaCLR/ImageNet/imagenet_embeddings.py
applications/benchmarking/DynaCLR/OpenPhenom/config_template.yml
applications/benchmarking/DynaCLR/OpenPhenom/openphenom_embeddings.py
applications/contrastive_phenotyping/evaluation/ALFI_MSD_v2.py
applications/contrastive_phenotyping/evaluation/PC_vs_computed_features.py
applications/contrastive_phenotyping/evaluation/analyze_embeddings.py
applications/contrastive_phenotyping/evaluation/compute_pca_features.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/imagenet_pretrained_features.py
applications/contrastive_phenotyping/evaluation/knowledge_distillation.py
applications/contrastive_phenotyping/evaluation/knowledge_distillation_teacher.py
applications/contrastive_phenotyping/evaluation/linear_probing.py
applications/contrastive_phenotyping/evaluation/log_regresssion_training.py
applications/contrastive_phenotyping/evaluation/plot_embeddings.py
applications/contrastive_phenotyping/evaluation/time_decay_knn.py
applications/contrastive_phenotyping/figures/cell_division.py
applications/contrastive_phenotyping/figures/figure.mplstyle
applications/contrastive_phenotyping/figures/figure_cell_infection.py
applications/contrastive_phenotyping/figures/grad_attr.py
applications/contrastive_phenotyping/figures/organelle_dynamics.py
applications/contrastive_phenotyping/figures/track_smoothness.py
applications/infection_classification/Infection_classification_2Dmodel.py
applications/infection_classification/Infection_classifier_accuracy.py
applications/infection_classification/README.md
applications/infection_classification/classify_infection_2D.py
applications/infection_classification/infection_classifier_testing.py
applications/infection_classification/predict_infection_classifier.py
applications/pseudotime_analysis/plotting_utils.py
applications/pseudotime_analysis/utils.py
applications/pseudotime_analysis/evaluation/compare_dtw_embeddings.py
applications/pseudotime_analysis/evaluation/dtw_compare_openphenom.py
applications/pseudotime_analysis/simulation/demo_dtw_cellfeatures.py
applications/pseudotime_analysis/simulation/demo_ndim_dtw.py
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_v2.png
docs/figures/phase_to_nuclei_membrane.png
docs/figures/phase_to_nuclei_membrane.svg
docs/figures/svideo_1.png
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docs/figures/vs_hf_demo.gif
docs/logo/viscy.svg
examples/DynaCLR/README.md
examples/DynaCLR/download_data.sh
examples/DynaCLR/setup.sh
examples/DynaCLR/DynaCLR-DENV-VS-Ph/README.md
examples/DynaCLR/DynaCLR-DENV-VS-Ph/demo_infection.py
examples/DynaCLR/DynaCLR-DENV-VS-Ph/utils.py
examples/DynaCLR/DynaCLR-classical-sampling/README.md
examples/DynaCLR/DynaCLR-classical-sampling/create_pseudo_tracks.py
examples/DynaCLR/embedding-web-visualization/README.md
examples/DynaCLR/embedding-web-visualization/interactive_visualizer.py
examples/DynaCLR/embedding-web-visualization/demo_imgs/demo2_embedding_visualization_cluster.png
examples/DynaCLR/embedding-web-visualization/demo_imgs/demo2_embeddings_visualization_track.png
examples/DynaCLR/examples_cli/dynaclr_microglia_onnx.yml
examples/DynaCLR/examples_cli/fit.yml
examples/DynaCLR/examples_cli/fit_slurm.sh
examples/DynaCLR/examples_cli/predict.yml
examples/DynaCLR/examples_cli/predict_slurm.sh
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
examples/virtual_staining/vcp_tutorials/README.md
examples/virtual_staining/vcp_tutorials/hek293t.ipynb
examples/virtual_staining/vcp_tutorials/hek293t.py
examples/virtual_staining/vcp_tutorials/neuromast.ipynb
examples/virtual_staining/vcp_tutorials/neuromast.py
examples/virtual_staining/vcp_tutorials/quick_start.ipynb
examples/virtual_staining/vcp_tutorials/quick_start.py
tests/__init__.py
tests/conftest.py
tests/data/__init__.py
tests/data/test_hcs.py
tests/data/test_select.py
tests/data/test_triplet.py
tests/evaluation/__init__.py
tests/evaluation/test_cell_feature_metrics.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_feature.py
tests/representation/test_lca.py
tests/translation/__init__.py
tests/translation/test_engine.py
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
tests/utils/test_aux_utils.py
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
viscy.egg-info/requires.txt
viscy.egg-info/top_level.txt
viscy/data/__init__.py
viscy/data/cell_classification.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/select.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/representation/classification.py
viscy/representation/contrastive.py
viscy/representation/embedding_writer.py
viscy/representation/engine.py
viscy/representation/multi_modal.py
viscy/representation/evaluation/__init__.py
viscy/representation/evaluation/clustering.py
viscy/representation/evaluation/dimensionality_reduction.py
viscy/representation/evaluation/distance.py
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viscy/representation/evaluation/lca.py
viscy/representation/evaluation/visualization.py
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
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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
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viscy/utils/slurm_utils.py