├── .dockerignore ├── .github ├── FUNDING.yml └── workflows │ └── python-app.yml ├── .gitignore ├── .pylintrc ├── .readthedocs.yaml ├── .travis.yml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── chunkflow ├── __init__.py ├── __main__.py ├── __version__.py ├── chunk │ ├── __init__.py │ ├── affinity_map │ │ ├── __init__.py │ │ └── base.py │ ├── base.py │ ├── image │ │ ├── __init__.py │ │ ├── adjust_grey.py │ │ └── base.py │ ├── probability_map.py │ ├── segmentation.py │ └── validate.py ├── flow │ ├── __init__.py │ ├── base.py │ ├── divid_conquer │ │ ├── __init__.py │ │ ├── inferencer.py │ │ ├── patch │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── identity.py │ │ │ ├── patch_mask.py │ │ │ ├── pytorch.py │ │ │ ├── pznet.py │ │ │ └── universal.py │ │ └── transform.py │ ├── downsample_upload.py │ ├── flow.py │ ├── load_pngs.py │ ├── load_precomputed.py │ ├── log_summary.py │ ├── mask.py │ ├── mesh.py │ ├── mesh_manifest.py │ ├── napari.py │ ├── neuroglancer.py │ ├── plugin.py │ ├── save_pngs.py │ ├── save_precomputed.py │ ├── setup_env.py │ └── view.py ├── lib │ ├── __init__.py │ ├── aws │ │ ├── __init__.py │ │ └── sqs_queue.py │ ├── cartesian_coordinate.py │ ├── flow.py │ ├── gala │ │ ├── __init__.py │ │ └── evaluate.py │ ├── igneous │ │ ├── __init__.py │ │ ├── downsample.py │ │ ├── downsample_scales.py │ │ └── tasks.py │ ├── region_of_interest.py │ └── utils.py ├── plugins │ ├── agglomerate.py │ ├── aggregate_skeleton_fragments.py │ ├── aws │ │ ├── cloud_watch.py │ │ └── test_cloud_watch.py │ ├── clahe.py │ ├── cutout_dvid_label.py │ ├── czann_inference.py │ ├── detect_points.py │ ├── fill_segmentation_holes.py │ ├── gaussian_filter.py │ ├── inverse.py │ ├── load_mrc.py │ ├── load_n5.py │ ├── load_nrrd.py │ ├── load_tensorstore.py │ ├── mapto01.py │ ├── median_filter.py │ ├── napari_pixel_classifier.py │ ├── print_max_id.py │ ├── requirements.txt │ ├── rescale_intensity.py │ ├── save_nrrd.py │ ├── skeletonize.py │ ├── statistics.py │ ├── stretch_intensity.py │ ├── synapse │ │ ├── adjust_pre.py │ │ ├── detect_duplicate_post.py │ │ ├── detect_post_synapses.py │ │ ├── detect_pre_synapses.py │ │ └── find_tbar_object.py │ └── transpose.py ├── point_cloud.py ├── pyproject.toml ├── synapses.py └── volume.py ├── conftest.py ├── count_operators.sh ├── dev-environments.txt ├── distributed ├── kubernetes │ ├── .dockerignore │ ├── README.md │ ├── connect_to_cluster.sh │ └── deploy.yml └── restapi │ ├── server.py │ ├── task.py │ └── worker.py ├── docker ├── base │ └── Dockerfile └── inference │ └── Dockerfile.pytorch ├── docs ├── Makefile ├── README.md ├── logo │ ├── CMYK_print │ │ ├── Chunkflow_logo_CMYK.eps │ │ ├── Chunkflow_logo_CMYK.jpg │ │ ├── Chunkflow_logo_CMYK.pdf │ │ └── Chunkflow_logo_CMYK.png │ └── RGB_web │ │ ├── Chunkflow_logo_RBG.eps │ │ ├── Chunkflow_logo_RBG.jpg │ │ ├── Chunkflow_logo_RBG.png │ │ └── Chunkflow_logo_RBG.svg ├── make.bat ├── requirements.txt └── source │ ├── _static │ ├── custom.css │ └── image │ │ ├── cleft.png │ │ ├── cleft_label.png │ │ ├── cremi_image.png │ │ ├── image_aff.png │ │ ├── image_seg.png │ │ ├── log_summary.png │ │ ├── operator_list.png │ │ ├── random_image_in_cloudvolume_viewer.png │ │ ├── random_image_in_neuroglancer.png │ │ └── tasks_in_sqs.png │ ├── api.rst │ ├── conf.py │ ├── development.rst │ ├── index.rst │ ├── install.rst │ ├── introduction.rst │ └── tutorial.rst ├── examples ├── downsample │ ├── create_tasks.sh │ └── downsample.sh ├── inference │ ├── 01_download.sh │ ├── batchnorm3d_to_instancenorm3d.py │ ├── inference.sh │ ├── universal_identity.py │ ├── universal_pytorch.py │ └── universal_pznet.py └── mesh │ ├── create_tasks.sh │ ├── manifest.sh │ └── mesh.sh ├── requirements.txt ├── setup.py └── tests ├── __init__.py ├── chunk ├── __init__.py ├── affinity_map │ └── test_affinity_map.py ├── image │ ├── __init__.py │ ├── test_adjust_grey.py │ └── test_image.py ├── segmentation │ ├── __init__.py │ └── test_segmentation.py ├── test_chunk.py └── test_validate.py ├── command_line.sh ├── data ├── levels │ ├── 1 │ │ └── 26774 │ └── normalized.npz └── log │ ├── 0-3_16384-16492_86294-88342_121142-123190.json │ └── 0-3_16384-16492_88342-90390_110902-112950.json ├── flow ├── __init__.py ├── divid_conquer │ ├── __init__.py │ ├── test_inferencer.py │ ├── test_patch_mask.py │ └── visualize_transform.py ├── test_downsample_upload.py ├── test_flow.py ├── test_load_precomputed.py ├── test_load_save.py ├── test_mesh.py ├── test_normalize_section_contrast.py └── test_save_precomputed.py ├── lib ├── aws │ ├── __init__.py │ └── test_sqs_queue.py ├── sp3_bboxes.txt ├── test_cartesian_coordinate.py └── test_synapses.py ├── requirements.txt ├── test_command_line.py └── test_volume.py /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seung-lab/chunkflow/HEAD/.dockerignore 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