├── .github └── workflows │ ├── publish.yaml │ └── tests.yaml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── docker ├── Dockerfile └── Makefile ├── lsd ├── __init__.py ├── post │ ├── __init__.py │ ├── agglomerate.py │ ├── find_connected_components.h │ ├── fragments.py │ ├── graph_merge.py │ ├── local_segmentation.py │ ├── merge_tree.pyx │ ├── parallel_aff_agglomerate.py │ ├── parallel_fragments.py │ ├── parallel_lsd_agglomerate.py │ ├── persistence │ │ ├── __init__.py │ │ ├── mongodb_rag_provider.py │ │ └── sqlite_rag_provider.py │ ├── rag.py │ └── shared_rag_provider.py ├── train │ ├── __init__.py │ ├── gp │ │ ├── __init__.py │ │ └── add_local_shape_descriptor.py │ └── local_shape_descriptor.py └── tutorial │ ├── example_nets │ └── fib25 │ │ ├── acrlsd │ │ ├── mknet.py │ │ ├── predict.py │ │ └── train.py │ │ ├── lsd │ │ ├── mknet.py │ │ ├── predict.py │ │ └── train.py │ │ ├── mtlsd │ │ ├── mknet.py │ │ ├── predict.py │ │ └── train.py │ │ └── vanilla │ │ ├── mknet.py │ │ ├── predict.py │ │ ├── train.py │ │ └── train_pytorch.py │ ├── notebooks │ ├── basic_gp_tutorial.ipynb │ ├── inference.ipynb │ ├── lsd_data_download.ipynb │ ├── quick_tutorial.ipynb │ ├── segment.ipynb │ ├── train_affinities.ipynb │ ├── train_lsds.ipynb │ ├── train_lsds_ignore_glia.ipynb │ ├── train_lsds_non_em_pytorch.ipynb │ ├── train_lsds_sparse_labels.ipynb │ └── train_mtlsd.ipynb │ └── scripts │ ├── 01_predict_blockwise.py │ ├── 02_extract_fragments_blockwise.py │ ├── 03_agglomerate_blockwise.py │ ├── 04_find_segments.py │ ├── 05_evaluate_annotations.py │ ├── 05_evaluate_volumes.py │ ├── 05_extract_segmentation_from_lut.py │ └── workers │ ├── agglomerate_worker.py │ └── extract_fragments_worker.py ├── pyproject.toml ├── requirements-dev.txt ├── requirements.txt ├── setup.py ├── singularity ├── Makefile └── Singularity └── tests ├── test_components.py ├── test_pipeline.py ├── test_shape_descriptor.py ├── test_strided.py └── test_synthetic.py /.github/workflows/publish.yaml: 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