├── .github ├── dependabot.yml └── workflows │ └── main.yml ├── .gitignore ├── .pylintrc ├── .readthedocs.yaml ├── LICENSE.txt ├── README.md ├── bin ├── build_bf.sh ├── build_deps.bat ├── build_deps.sh ├── build_docs.sh ├── build_jb.bat ├── build_jb.sh ├── build_jre.bat ├── build_jre.sh ├── build_se.bat ├── build_se.sh ├── deploy.sh ├── entitlements.plist ├── libmag.sh ├── packager.nsi ├── pipelines.sh ├── process_nohup.sh ├── runaltpy.sh ├── sample_cmds.sh ├── sample_cmds_bash.ipynb ├── sample_settings.sh ├── setup_conda ├── setup_conda.bat ├── setup_cxfreeze.py ├── setup_multi_venvs.bat ├── setup_multi_venvs.sh ├── setup_pyinstaller.spec ├── setup_server.sh ├── setup_venv.bat ├── setup_venv.sh ├── stitch.sh └── surf_clean.sh ├── clrstats ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── clrstats.R │ ├── jitter_plot.R │ └── volcano_plot.R ├── run.R └── stats.Rproj ├── docker ├── buildse │ └── Dockerfile ├── miniconda3 │ └── Dockerfile ├── ubuntu1604 │ └── Dockerfile ├── ubuntu1604_venv │ └── Dockerfile └── ubuntu1804 │ └── Dockerfile ├── docs ├── Makefile ├── cli.md ├── cloud_aws.md ├── conf.py ├── index.rst ├── install.md ├── load.md ├── make.bat ├── modules.rst ├── pipelines.md ├── release │ ├── index.md │ ├── release_template.md │ ├── release_v0.9.md │ ├── release_v1.0.md │ ├── release_v1.1.md │ ├── release_v1.2.md │ ├── release_v1.3.md │ ├── release_v1.4.md │ ├── release_v1.5.md │ ├── release_v1.6.md │ └── release_v1.7.md ├── settings.md ├── stitch.rst └── viewers.md ├── environment.yml ├── envs ├── environment_all.yml ├── environment_rel.yml ├── requirements.txt ├── requirements_py36 ├── requirements_py37 └── requirements_py38 ├── images ├── magmap.icns ├── magmap.ico └── magmap.png ├── magmap ├── __init__.py ├── atlas │ ├── __init__.py │ ├── atlas_refiner.py │ ├── edge_seg.py │ ├── labels_meta.py │ ├── ontology.py │ ├── reg_tasks.py │ ├── register.py │ └── transformer.py ├── brain_globe │ ├── __init__.py │ ├── bg_controller.py │ └── bg_model.py ├── cloud │ ├── __init__.py │ ├── aws.py │ └── notify.py ├── cv │ ├── __init__.py │ ├── chunking.py │ ├── classifier.py │ ├── colocalizer.py │ ├── cv_nd.py │ ├── detector.py │ ├── segmenter.py │ ├── stack_detect.py │ └── verifier.py ├── gui │ ├── __init__.py │ ├── atlas_editor.py │ ├── atlas_threads.py │ ├── event_handlers.py │ ├── image_viewer.py │ ├── import_threads.py │ ├── pixel_display.py │ ├── plot_editor.py │ ├── roi_editor.py │ ├── verifier_editor.py │ ├── vis_3d.py │ ├── vis_handler.py │ └── visualizer.py ├── io │ ├── __init__.py │ ├── cli.py │ ├── df_io.py │ ├── export_regions.py │ ├── export_rois.py │ ├── export_stack.py │ ├── importer.py │ ├── libmag.py │ ├── load_env.py │ ├── naming.py │ ├── np_io.py │ ├── packaging.py │ ├── sitk_io.py │ ├── sqlite.py │ ├── subproc_io.py │ └── yaml_io.py ├── plot │ ├── __init__.py │ ├── colormaps.py │ ├── plot_2d.py │ ├── plot_3d.py │ └── plot_support.py ├── settings │ ├── __init__.py │ ├── atlas_prof.py │ ├── config.py │ ├── grid_search_prof.py │ ├── logs.py │ ├── prefs_prof.py │ ├── profiles.py │ └── roi_prof.py ├── stats │ ├── __init__.py │ ├── atlas_stats.py │ ├── clustering.py │ ├── mlearn.py │ └── vols.py └── tests │ ├── __init__.py │ ├── test_chunking.py │ ├── test_classifier.py │ ├── test_cv_nd.py │ ├── test_detector.py │ ├── test_image_stack_integration.py │ ├── test_img_equality.py │ ├── test_libmag.py │ ├── test_np_io.py │ └── test_visualizer.py ├── profiles ├── atlas_reg.yaml ├── atlas_rotate.yml ├── grid_sizes.yaml └── roi_blobs.yaml ├── pyproject.toml ├── run.py ├── stitch ├── ij_bigstitch.py ├── ij_stitch.py ├── mesospim_to_tif.py └── tile_config.py └── surfaces └── decimate_1pct.mlx /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanderslab/magellanmapper/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/main.yml: 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