├── .github └── workflows │ └── build_and_test.yaml ├── .gitignore ├── LICENSE ├── README.md ├── cluster_tools ├── __init__.py ├── affinities │ ├── __init__.py │ ├── embedding_distances.py │ ├── gradients.py │ ├── insert_affinities.py │ ├── insert_affinities_workflow.py │ └── to_boundaries.py ├── agglomerative_clustering │ ├── __init__.py │ └── agglomerative_clustering.py ├── bigcat │ ├── __init__.py │ └── bigcat_workflow.py ├── cluster_tasks.py ├── connected_components │ ├── __init__.py │ ├── connected_component_blocks.py │ ├── connected_components_workflow.py │ ├── merge_assignments.py │ └── merge_faces.py ├── copy_sources │ ├── __init__.py │ └── copy_sources.py ├── copy_volume │ ├── __init__.py │ └── copy_volume.py ├── costs │ ├── __init__.py │ ├── costs_workflow.py │ ├── predict.py │ └── probs_to_costs.py ├── debugging │ ├── __init__.py │ ├── check_components.py │ ├── check_sub_graphs.py │ ├── check_sub_graphs_workflow.py │ └── check_ws_workflow.py ├── distances │ ├── __init__.py │ ├── distance_workflow.py │ └── object_distances.py ├── downscaling │ ├── __init__.py │ ├── downscaling.py │ ├── downscaling_workflow.py │ ├── scale_to_boundaries.py │ └── upscaling.py ├── evaluation │ ├── __init__.py │ ├── evaluation_workflow.py │ ├── measures.py │ ├── object_iou.py │ └── object_vi.py ├── features │ ├── __init__.py │ ├── block_edge_features.py │ ├── features_workflow.py │ ├── image_filter.py │ ├── merge_edge_features.py │ ├── merge_region_features.py │ └── region_features.py ├── graph │ ├── __init__.py │ ├── graph_workflow.py │ ├── initial_sub_graphs.py │ ├── map_edge_ids.py │ └── merge_sub_graphs.py ├── ilastik │ ├── __init__.py │ ├── carving.py │ ├── ilastik_workflow.py │ ├── prediction.py │ └── stack_predictions.py ├── inference │ ├── __init__.py │ ├── frameworks.py │ ├── inference.py │ ├── inference_embl.py │ ├── multiscale_inference.py │ ├── multiscale_inference_vis.py │ └── prep_model.py ├── label_multisets │ ├── __init__.py │ ├── create_multiset.py │ ├── downscale_multiset.py │ └── label_multiset_workflow.py ├── learning │ ├── __init__.py │ ├── edge_labels.py │ ├── learn_rf.py │ └── learning_workflow.py ├── lifted_features │ ├── __init__.py │ ├── clear_lifted_edges_from_labels.py │ ├── costs_from_node_labels.py │ ├── lifted_feature_workflow.py │ ├── merge_lifted_problems.py │ └── sparse_lifted_neighborhood.py ├── lifted_multicut │ ├── __init__.py │ ├── lifted_multicut_workflow.py │ ├── reduce_lifted_problem.py │ ├── solve_lifted_global.py │ └── solve_lifted_subproblems.py ├── masking │ ├── __init__.py │ ├── blocks_from_mask.py │ ├── blocks_from_mask_workflow.py │ └── minfilter.py ├── meshes │ ├── __init__.py │ ├── compute_meshes.py │ └── mesh_workflow.py ├── morphology │ ├── __init__.py │ ├── block_morphology.py │ ├── merge_morphology.py │ ├── morphology_workflow.py │ └── region_centers.py ├── multicut │ ├── __init__.py │ ├── multicut_workflow.py │ ├── reduce_problem.py │ ├── solve_global.py │ ├── solve_subproblems.py │ └── sub_solutions.py ├── mutex_watershed │ ├── __init__.py │ ├── mws_blocks.py │ ├── mws_workflow.py │ ├── two_pass_assignments.py │ └── two_pass_mws.py ├── node_labels │ ├── __init__.py │ ├── block_node_labels.py │ ├── merge_node_labels.py │ └── node_label_workflow.py ├── paintera │ ├── __init__.py │ ├── assignments.py │ ├── conversion_workflow.py │ ├── label_block_mapping.py │ └── unique_block_labels.py ├── postprocess │ ├── __init__.py │ ├── background_size_filter.py │ ├── filling_size_filter.py │ ├── filter_blocks.py │ ├── graph_connected_components.py │ ├── graph_watershed_assignments.py │ ├── id_filter.py │ ├── orphan_assignments.py │ ├── postprocess_workflow.py │ └── size_filter_blocks.py ├── relabel │ ├── __init__.py │ ├── find_labeling.py │ ├── find_uniques.py │ ├── merge_uniques.py │ └── relabel_workflow.py ├── skeletons │ ├── __init__.py │ ├── skeleton_evaluation.py │ ├── skeleton_workflow.py │ ├── skeletonize.py │ └── upsample_skeletons.py ├── statistics │ ├── __init__.py │ ├── block_statistics.py │ ├── merge_statistics.py │ └── statistics_workflow.py ├── stitching │ ├── __init__.py │ ├── simple_stitch_assignments.py │ ├── simple_stitch_edges.py │ ├── stitch_faces.py │ ├── stitching_multicut.py │ └── stitching_workflows.py ├── threshold │ ├── __init__.py │ └── threshold.py ├── transformations │ ├── __init__.py │ ├── affine.py │ ├── linear.py │ ├── transformation_workflows.py │ ├── transformix.py │ └── transformix_coordinate.py ├── utils │ ├── __init__.py │ ├── function_utils.py │ ├── parse_utils.py │ ├── task_utils.py │ └── volume_utils.py ├── version.py ├── watershed │ ├── __init__.py │ ├── agglomerate.py │ ├── slice_agglomeration.py │ ├── two_pass_watershed.py │ ├── watershed.py │ ├── watershed_from_seeds.py │ └── watershed_workflow.py ├── workflows.py └── write │ ├── __init__.py │ └── write.py ├── conda-recipe └── meta.yaml ├── environment.yml ├── example ├── README.md ├── downscale.py ├── ilastik │ └── carving.py ├── multicut.py ├── postprocessing.py └── skeletons.py ├── publications └── leveraging_domain_knowledge │ ├── 1_axon_dendrite_attribution │ ├── 0_data.py │ ├── 1_multicut_full.py │ ├── 1_multicut_simple.py │ ├── 2_lifted_multicut_full.py │ ├── 2_lifted_multicut_simple.py │ ├── 3_evaluation.py │ ├── 4_view_results.py │ └── README.md │ ├── 2_false_merge_detection │ ├── 1_prediction.py │ ├── 2_multicut.py │ ├── 3_skeletonize.py │ ├── 4_oracle.py │ ├── 5_roc.py │ ├── evaluate │ │ ├── __init__.py │ │ ├── copy_and_crop.py │ │ └── evaluate_fib.py │ ├── make_roc_fig.py │ ├── resolve_jointly.py │ ├── resolve_separately.py │ └── resolving │ │ ├── __init__.py │ │ ├── edges_from_skeletons.py │ │ ├── edges_to_problem.py │ │ ├── io.py │ │ ├── problem_workflow.py │ │ ├── resolve_individual_objects.py │ │ └── resolving_workflow.py │ ├── 3_instance_segmentation_of_small_organelles │ ├── 1_prediction.py │ ├── 2_extract_boundaries.py │ ├── 3_segment.py │ └── 4_validate.py │ ├── 4_nucleus_segmentation │ ├── 1_watershed.py │ ├── 2_mc.py │ ├── 3_lmc.py │ └── 4_evaluate.py │ ├── 5_lifted_solver │ ├── eval_solvers.py │ ├── extract_test_data.py │ ├── initial_multicut.py │ ├── run_solvers.py │ └── set_up_problem.py │ └── README.md ├── run_all_tests.sh ├── setup.py ├── test ├── __init__.py ├── base.py ├── connected_components │ ├── __init__.py │ └── connected_components.py ├── downscaling │ ├── __init__.py │ └── test_downscaling.py ├── evaluation │ ├── __init__.py │ └── test_evaluation.py ├── features │ ├── __init__.py │ ├── test_edge_features.py │ └── test_region_features.py ├── graph │ ├── __init__.py │ └── test_graph.py ├── ilastik │ └── test_pixel_classification.py ├── inference │ └── test_inference.py ├── label_multisets │ ├── __init__.py │ └── test_label_multisets.py ├── lifted_features │ ├── __init__.py │ ├── lifted_features.py │ └── sparse_lifted_neighborhood.py ├── morphology │ ├── __init__.py │ └── test_morphology.py ├── mutex_watershed │ ├── __init__.py │ ├── test_mws.py │ └── test_mws_with_mask.py ├── node_labels │ ├── __init__.py │ └── test_node_labels.py ├── postprocess │ ├── __init__.py │ └── test_postprocess.py ├── relabel │ ├── __init__.py │ └── test_relabel.py ├── retry │ ├── __init__.py │ ├── failing_task.py │ └── test_retry.py ├── skeletons │ ├── __init__.py │ └── test_skeletons.py ├── statistics │ ├── __init__.py │ └── test_statistics.py ├── transformations │ ├── __init__.py │ └── test_linear.py ├── utils │ ├── __init__.py │ ├── test_function_utils.py │ └── test_volume_utils.py ├── watershed │ ├── __init__.py │ ├── test_watershed_with_mask.py │ └── test_watershed_without_mask.py ├── workflows │ ├── __init__.py │ ├── lifted_multicut_workflow.py │ └── multicut_workflow.py └── write │ ├── __init__.py │ └── test_write.py └── test_data └── cremi-test-project.ilp /.github/workflows/build_and_test.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/constantinpape/cluster_tools/HEAD/.github/workflows/build_and_test.yaml 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