├── .editorconfig ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── custom.md │ └── feature_request.md ├── actions │ └── setup-python-env │ │ └── action.yaml └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docker ├── README.md ├── sopa-baysor │ └── Dockerfile ├── sopa-cellpose │ └── Dockerfile ├── sopa-comseg │ └── Dockerfile ├── sopa-proseg │ └── Dockerfile ├── sopa-stardist │ └── Dockerfile ├── sopa-tangram │ └── Dockerfile └── sopa │ └── Dockerfile ├── docs ├── README.md ├── api │ ├── aggregation.md │ ├── misc.md │ ├── patches.md │ ├── readers.md │ ├── segmentation.md │ ├── spatial.md │ └── utils.md ├── assets │ ├── example_tissue_segmentation.png │ ├── explorer │ │ ├── add_image.png │ │ ├── download_alignment.png │ │ ├── download_transformation_file.png │ │ ├── lasso.png │ │ ├── lasso2.png │ │ ├── leiden.png │ │ ├── multi_lasso.png │ │ └── post_overlay.png │ ├── napari_visium_hd.png │ ├── overview_white.png │ ├── sopa.png │ ├── sopa_favicon.png │ ├── sopa_small_blue.png │ └── sopa_small_white.png ├── cite_us.md ├── css │ ├── custom.css │ └── termynal.css ├── faq.md ├── getting_started.md ├── index.md ├── js │ ├── custom.js │ ├── mathjax.js │ └── termynal.js └── tutorials │ ├── align.ipynb │ ├── align.md │ ├── api_usage.ipynb │ ├── cli_usage.md │ ├── compare_segmentations.ipynb │ ├── comseg.ipynb │ ├── custom_segmentation.ipynb │ ├── he.ipynb │ ├── image_test_matrix.csv │ ├── multi_step_segmentation.md │ ├── snakemake.md │ ├── spatial.ipynb │ ├── techno_specific.md │ ├── visium_hd.ipynb │ └── xenium_explorer │ ├── Selection_1_cells_stats.csv │ ├── Selection_1_coordinates.csv │ ├── Selection_2_cells_stats.csv │ ├── coordinates.csv │ └── explorer.ipynb ├── mkdocs.yml ├── pyproject.toml ├── sopa ├── __init__.py ├── _logging.py ├── _settings.py ├── aggregation │ ├── __init__.py │ ├── aggregation.py │ ├── bins.py │ ├── channels.py │ ├── overlay.py │ └── transcripts.py ├── cli │ ├── annotate.py │ ├── app.py │ ├── explorer.py │ ├── patchify.py │ ├── resolve.py │ ├── segmentation.py │ └── utils.py ├── constants.py ├── io │ ├── __init__.py │ ├── explorer │ │ ├── __init__.py │ │ ├── _constants.py │ │ ├── converter.py │ │ ├── images.py │ │ ├── points.py │ │ ├── shapes.py │ │ ├── table.py │ │ └── utils.py │ ├── reader │ │ ├── __init__.py │ │ ├── _wsi_reader.py │ │ ├── _wsi_store.py │ │ ├── cosmx.py │ │ ├── generic.py │ │ ├── hyperion.py │ │ ├── macsima.py │ │ ├── merscope.py │ │ ├── molecular_cartography.py │ │ ├── phenocycler.py │ │ ├── utils.py │ │ ├── visium_hd.py │ │ ├── wsi.py │ │ └── xenium.py │ ├── report │ │ ├── __init__.py │ │ ├── css.py │ │ ├── engine.py │ │ └── generate.py │ └── standardize.py ├── main.py ├── patches │ ├── __init__.py │ ├── cluster.py │ ├── factory.py │ ├── infer.py │ ├── loader.py │ ├── models │ │ ├── __init__.py │ │ ├── conch.py │ │ ├── dinov2.py │ │ ├── dummy.py │ │ ├── histo_ssl.py │ │ ├── hoptimus0.py │ │ └── resnet.py │ ├── patches.py │ └── transcripts.py ├── segmentation │ ├── __init__.py │ ├── _tissue.py │ ├── methods │ │ ├── __init__.py │ │ ├── _baysor.py │ │ ├── _cellpose.py │ │ ├── _comseg.py │ │ ├── _custom.py │ │ ├── _dummy.py │ │ ├── _proseg.py │ │ ├── _stardist.py │ │ └── utils.py │ ├── resolve.py │ └── stainings.py ├── shapes │ ├── __init__.py │ ├── _rasterize.py │ ├── _vectorize.py │ ├── expand.py │ └── validate.py ├── spatial │ ├── __init__.py │ ├── _graph.py │ ├── build.py │ ├── distance.py │ ├── join.py │ └── morpho.py └── utils │ ├── __init__.py │ ├── annotation.py │ ├── data.py │ ├── image.py │ └── utils.py ├── tests ├── CMU-1-Small-Region.svs ├── compare_cv2_skimage.py ├── mask_example.npy ├── test_aggregation.py ├── test_converter.py ├── test_patches.py ├── test_rasterize.py ├── test_segmentation.py ├── test_shapes.py ├── test_spatial_operations.py ├── test_toy_snakemake.sh ├── test_transformations.py ├── test_utils.py ├── test_vectorize.py ├── test_wsi_backends.py ├── test_wsi_embeddings.py └── toy_tangram_ref.h5ad ├── uv.lock └── workflow ├── README.md ├── Snakefile ├── config ├── README.md ├── cosmx │ ├── baysor.yaml │ ├── cellpose.yaml │ ├── cellpose_baysor.yaml │ └── proseg.yaml ├── example_commented.yaml ├── hyperion │ └── base.yaml ├── macsima │ └── base.yaml ├── merscope │ ├── README.md │ ├── baysor_cellpose.yaml │ ├── baysor_vizgen.yaml │ ├── cellpose.yaml │ └── proseg.yaml ├── misc │ ├── custom_visium_hd.yaml │ ├── custom_xenium.yaml │ └── ome_tif.yaml ├── phenocycler │ ├── README.md │ ├── base_10X.yaml │ ├── base_20X.yaml │ └── base_40X.yaml ├── toy │ ├── backward_comp_check.yaml │ ├── baysor.yaml │ ├── baysor_overlaps.yaml │ ├── baysor_vizgen.yaml │ ├── baysor_with_sc.yaml │ ├── cellpose.yaml │ ├── cellpose_baysor.yaml │ ├── cellpose_comseg.yaml │ ├── cellpose_gpu.yaml │ ├── cellpose_proseg.yaml │ ├── comseg.yaml │ ├── proseg.yaml │ ├── proseg_3d.yaml │ └── tissue_cellpose.yaml ├── visium_hd │ ├── proseg.yaml │ ├── proseg_10x_website.yaml │ └── stardist.yaml └── xenium │ ├── baysor.yaml │ ├── baysor_prior.yaml │ ├── baysor_prior_small_cells.yaml │ ├── cellpose.yaml │ ├── cellpose_baysor.yaml │ └── proseg.yaml ├── profile ├── README.md ├── ci │ └── config.yaml ├── local │ └── config.yaml ├── lsf │ ├── README.md │ └── config.yaml ├── slurm-igr │ ├── README.md │ └── config.yaml └── slurm │ └── config.yaml ├── rules ├── baysor.smk ├── cellpose.smk ├── comseg.smk ├── proseg.smk ├── stardist.smk └── utils.smk ├── slurm ├── README.md └── config.yaml └── src ├── __init__.py ├── args.py ├── constants.py ├── paths.py └── validation.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gustaveroussy/sopa/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 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