├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── build-docs.yml │ ├── build-main.yml │ ├── publish.yml │ ├── test-and-lint-manual-trigger.yml │ └── test-and-lint.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── aicssegmentation ├── __init__.py ├── assets │ ├── diagrams │ │ ├── actb.png │ │ ├── actn1.png │ │ ├── atp2a2.png │ │ ├── cetn2.png │ │ ├── ctnnb1.png │ │ ├── dsp.png │ │ ├── fbl.png │ │ ├── gja1.png │ │ ├── h2b_interphase.png │ │ ├── lamp1.png │ │ ├── lmnb1_interphase.png │ │ ├── lmnb1_mitotic.png │ │ ├── myh10.png │ │ ├── npm1.png │ │ ├── nup153.png │ │ ├── pxn.png │ │ ├── rab5a.png │ │ ├── sec61b.png │ │ ├── slc25a17.png │ │ ├── smc1a.png │ │ ├── son.png │ │ ├── st6gal1.png │ │ ├── tjp1.png │ │ ├── tomm20.png │ │ └── tuba1b.png │ └── thumbnails │ │ ├── actb_post.png │ │ ├── actb_pre.png │ │ ├── actn1_post.png │ │ ├── actn1_pre.png │ │ ├── atp2a2_post.png │ │ ├── atp2a2_pre.png │ │ ├── cetn2_post.png │ │ ├── cetn2_pre.png │ │ ├── ctnnb1_post.png │ │ ├── ctnnb1_pre.png │ │ ├── dsp_post.png │ │ ├── dsp_pre.png │ │ ├── fbl_post.png │ │ ├── fbl_pre.png │ │ ├── gja1_post.png │ │ ├── gja1_pre.png │ │ ├── h2b_interphase_post.png │ │ ├── h2b_interphase_pre.png │ │ ├── lamp1_post.png │ │ ├── lamp1_pre.png │ │ ├── lmnb1_interphase_post.png │ │ ├── lmnb1_interphase_pre.png │ │ ├── lmnb1_mitotic_post.png │ │ ├── lmnb1_mitotic_pre.png │ │ ├── myh10_post.png │ │ ├── myh10_pre.png │ │ ├── npm1_post.png │ │ ├── npm1_pre.png │ │ ├── nup153_post.png │ │ ├── nup153_pre.png │ │ ├── pxn_post.png │ │ ├── pxn_pre.png │ │ ├── rab5a_post.png │ │ ├── rab5a_pre.png │ │ ├── sec61b_post.png │ │ ├── sec61b_pre.png │ │ ├── slc25a17_post.png │ │ ├── slc25a17_pre.png │ │ ├── smc1a_post.png │ │ ├── smc1a_pre.png │ │ ├── son_post.png │ │ ├── son_pre.png │ │ ├── st6gal1_post.png │ │ ├── st6gal1_pre.png │ │ ├── tjp1_post.png │ │ ├── tjp1_pre.png │ │ ├── tomm20_post.png │ │ ├── tomm20_pre.png │ │ ├── tuba1b_post.png │ │ └── tuba1b_pre.png ├── bin │ ├── __init__.py │ └── batch_processing.py ├── cli │ ├── __init__.py │ └── to_analysis.py ├── core │ ├── MO_threshold.py │ ├── __init__.py │ ├── hessian.py │ ├── output_utils.py │ ├── pre_processing_utils.py │ ├── seg_dot.py │ ├── utils.py │ ├── vessel.py │ └── visual.py ├── exceptions.py ├── structure_wrapper │ ├── __init__.py │ ├── seg_PCNA_earlyS_midS.py │ ├── seg_PCNA_lateS.py │ ├── seg_PCNA_lateS_hole_fill.py │ ├── seg_actb.py │ ├── seg_actn1.py │ ├── seg_atp2a2.py │ ├── seg_cardio_actn2.py │ ├── seg_cardio_atp2a2.py │ ├── seg_cardio_fbl.py │ ├── seg_cardio_fbl_100x.py │ ├── seg_cardio_myl7.py │ ├── seg_cardio_npm1.py │ ├── seg_cardio_npm1_100x.py │ ├── seg_cardio_tnni1.py │ ├── seg_cardio_ttn.py │ ├── seg_cetn2.py │ ├── seg_ctnnb1.py │ ├── seg_drug_npm1.py │ ├── seg_dsp.py │ ├── seg_fbl.py │ ├── seg_fbl_labelfree_4dn.py │ ├── seg_gja1.py │ ├── seg_h2b_interphase.py │ ├── seg_lamp1.py │ ├── seg_lmnb1_interphase.py │ ├── seg_lmnb1_mitotic.py │ ├── seg_myh10.py │ ├── seg_npm1.py │ ├── seg_npm1_SR.py │ ├── seg_npm_labelfree_4dn.py │ ├── seg_nup153.py │ ├── seg_polr2a.py │ ├── seg_polr2a_blob.py │ ├── seg_pxn.py │ ├── seg_rab5a.py │ ├── seg_sec61b.py │ ├── seg_sec61b_dual.py │ ├── seg_slc25a17.py │ ├── seg_smc1a.py │ ├── seg_son.py │ ├── seg_st6gal1.py │ ├── seg_template.py │ ├── seg_terf2.py │ ├── seg_tjp1.py │ ├── seg_tomm20.py │ ├── seg_tuba1b.py │ ├── seg_ubtf.py │ └── structure_segmenter.py ├── structure_wrapper_config │ ├── __init__.py │ ├── all_functions.json │ ├── conf_actb.json │ ├── conf_actn1.json │ ├── conf_atp2a2.json │ ├── conf_cetn2.json │ ├── conf_ctnnb1.json │ ├── conf_dsp.json │ ├── conf_fbl.json │ ├── conf_gja1.json │ ├── conf_h2b_interphase.json │ ├── conf_lamp1.json │ ├── conf_lmnb1_interphase.json │ ├── conf_lmnb1_mitotic.json │ ├── conf_myh10.json │ ├── conf_npm1.json │ ├── conf_nup153.json │ ├── conf_pxn.json │ ├── conf_rab5a.json │ ├── conf_sec61b.json │ ├── conf_slc25a17.json │ ├── conf_smc1a.json │ ├── conf_son.json │ ├── conf_st6gal1.json │ ├── conf_tjp1.json │ ├── conf_tomm20.json │ ├── conf_tuba1b.json │ └── function_params.md ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── resources │ │ └── images │ │ │ ├── expected_actb_struct_segmentation.tiff │ │ │ ├── expected_actn1_struct_segmentation.tiff │ │ │ ├── expected_atp2a2_struct_segmentation.tiff │ │ │ ├── expected_cardio_actn2_struct_segmentation.tiff │ │ │ ├── expected_cardio_atp2a2_struct_segmentation.tiff │ │ │ ├── expected_cardio_fbl_100x_struct_segmentation.tiff │ │ │ ├── expected_cardio_fbl_struct_segmentation.tiff │ │ │ ├── expected_cardio_myl7_struct_segmentation.tiff │ │ │ ├── expected_cardio_npm1_100x_struct_segmentation.tiff │ │ │ ├── expected_cardio_npm1_struct_segmentation.tiff │ │ │ ├── expected_cardio_tnni1_struct_segmentation.tiff │ │ │ ├── expected_cardio_ttn_struct_segmentation.tiff │ │ │ ├── expected_cetn2_struct_segmentation.tiff │ │ │ ├── expected_ctnnb1_struct_segmentation.tiff │ │ │ ├── expected_drug_npm1_struct_segmentation.tiff │ │ │ ├── expected_dsp_struct_segmentation.tiff │ │ │ ├── expected_fbl_labelfree_4dn_struct_segmentation.tiff │ │ │ ├── expected_fbl_struct_segmentation.tiff │ │ │ ├── expected_gja1_struct_segmentation.tiff │ │ │ ├── expected_h2b_interphase_struct_segmentation.tiff │ │ │ ├── expected_lamp1_struct_segmentation.tiff │ │ │ ├── expected_lmnb1_interphase_struct_segmentation.tiff │ │ │ ├── expected_lmnb1_mitotic_struct_segmentation.tiff │ │ │ ├── expected_myh10_struct_segmentation.tiff │ │ │ ├── expected_npm1_struct_segmentation.tiff │ │ │ ├── expected_npm_labelfree_4dn_struct_segmentation.tiff │ │ │ ├── expected_nup153_struct_segmentation.tiff │ │ │ ├── expected_pxn_struct_segmentation.tiff │ │ │ ├── expected_rab5a_struct_segmentation.tiff │ │ │ ├── expected_sec61b_dual_struct_segmentation.tiff │ │ │ ├── expected_sec61b_struct_segmentation.tiff │ │ │ ├── expected_slc25a17_struct_segmentation.tiff │ │ │ ├── expected_smc1a_struct_segmentation.tiff │ │ │ ├── expected_son_struct_segmentation.tiff │ │ │ ├── expected_st6gal1_struct_segmentation.tiff │ │ │ ├── expected_terf2_struct_segmentation.tiff │ │ │ ├── expected_tjp1_struct_segmentation.tiff │ │ │ ├── expected_tomm20_struct_segmentation.tiff │ │ │ ├── expected_tuba1b_struct_segmentation.tiff │ │ │ ├── expected_ubtf_struct_segmentation.tiff │ │ │ └── random_input.tiff │ ├── test_config.py │ ├── test_structures.py │ └── workflow │ │ ├── __init__.py │ │ ├── mock_module.py │ │ ├── resources │ │ └── test │ │ │ └── test.tiff │ │ ├── test_all_workflows.py │ │ ├── test_batch_workflow.py │ │ ├── test_workflow.py │ │ ├── test_workflow_config.py │ │ ├── test_workflow_definition.py │ │ ├── test_workflow_engine.py │ │ └── test_workflow_step.py ├── util │ ├── __init__.py │ ├── directories.py │ ├── filesystem.py │ └── lazy.py └── workflow │ ├── __init__.py │ ├── batch_workflow.py │ ├── segmenter_function.py │ ├── workflow.py │ ├── workflow_config.py │ ├── workflow_definition.py │ ├── workflow_engine.py │ └── workflow_step.py ├── demo_data ├── RAB5_demo_data.tif ├── TNNI1_demo_data.tif ├── TOM20_demo_data.tif ├── TOMM20_pipeline_example_cell_segmentation.tiff ├── TOMM20_pipeline_example_nucleus_segmentation.tiff └── TOMM20_pipeline_example_structure_segmentation.tiff ├── docs ├── Makefile ├── conda_why.md ├── conf.py ├── contributing.rst ├── doc.rst ├── full.jpg ├── full_doc.md ├── full_mem.jpg ├── full_str.jpg ├── index.rst ├── installation.rst ├── installation_linux.md ├── installation_mac.md ├── installation_windows.md ├── jupyter_lookup_table.md ├── make.bat ├── object_identification.md ├── rab5a_raw.jpg ├── step1.jpg ├── step2.jpg ├── step3_p1.jpg └── step3_p2.jpg ├── lookup_table_demo ├── README.md ├── bridging_the_gap_between_binary_image_and_analysis.ipynb ├── demo_TNNI1.ipynb ├── playground_Sec61b.ipynb ├── playground_curvi.ipynb ├── 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