├── .github └── workflows │ └── main.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── annotations ├── location_group_mapping.tsv └── splits │ ├── test_antibodies.txt │ ├── train_antibodies.txt │ └── valid_antibodies.txt ├── configs ├── MAE-cellS-protS-byol.yaml ├── MAE-cellS-protS-contrast.yaml ├── MAE.yaml ├── cellS-protS.yaml ├── cellS.yaml └── protS.yaml ├── data ├── __init__.py ├── collate_fn.py ├── dataset.py ├── get_datasets.py └── utils.py ├── github_stats.py ├── main_lightning.py ├── models ├── __init__.py ├── attention_pooling.py ├── centroid_diff.py ├── focal_loss.py ├── get_models.py ├── lightning │ ├── __init__.py │ ├── base_mae.py │ ├── base_ssl.py │ ├── base_supervised.py │ ├── byol_ssl.py │ ├── callbacks │ │ ├── gc_callback.py │ │ └── result_callback.py │ ├── contrast_byol_mae.py │ ├── contrast_mae.py │ └── save_utils.py ├── ntxent.py ├── object_aware_mae.py ├── projectors.py └── vit.py ├── requirements.txt ├── resources └── arch.png ├── traffic ├── 2025-08-14 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-08-15 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-08-29 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-09-01 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-09-15 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-09-22 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-09-29 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-10-01 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-10-08 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-10-15 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-10-22 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-10-27 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-11-03 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-11-10 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-11-17 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-11-24 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-12-01 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json ├── 2025-12-08 │ ├── clones.json │ ├── paths.json │ ├── referrers.json │ └── views.json └── summary.csv └── utils ├── augmentations.py └── colormaps ├── blue.lut ├── green.lut ├── red.lut └── yellow.lut /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CellProfiling/subcell-embed/HEAD/.github/workflows/main.yml -------------------------------------------------------------------------------- /.gitignore: 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