{"id":20956503,"url":"https://github.com/bluebrain/atlas-direction-vectors","last_synced_at":"2025-05-14T05:31:51.111Z","repository":{"id":57412373,"uuid":"451806460","full_name":"BlueBrain/atlas-direction-vectors","owner":"BlueBrain","description":"Tools to compute direction vectors in the context of brain atlases.","archived":true,"fork":false,"pushed_at":"2025-02-26T13:07:06.000Z","size":239,"stargazers_count":3,"open_issues_count":4,"forks_count":3,"subscribers_count":39,"default_branch":"main","last_synced_at":"2025-04-28T08:47:37.263Z","etag":null,"topics":["atlas","build"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BlueBrain.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG.rst","contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.txt","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-01-25T09:05:43.000Z","updated_at":"2025-02-26T13:07:09.000Z","dependencies_parsed_at":"2024-01-16T16:59:18.148Z","dependency_job_id":"ebc063a1-b7f8-4163-bd08-21d379a2684e","html_url":"https://github.com/BlueBrain/atlas-direction-vectors","commit_stats":{"total_commits":18,"total_committers":5,"mean_commits":3.6,"dds":0.2777777777777778,"last_synced_commit":"d0b7331f2add43a9a3b185c9bc594f339daab01d"},"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-direction-vectors","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-direction-vectors/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-direction-vectors/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-direction-vectors/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/atlas-direction-vectors/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254076977,"owners_count":22010630,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["atlas","build"],"created_at":"2024-11-19T01:26:21.937Z","updated_at":"2025-05-14T05:31:51.097Z","avatar_url":"https://github.com/BlueBrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":".. warning::\n   The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.\n   Future development will take place at: https://github.com/openbraininstitute/atlas-direction-vectors\n\n|banner|\n\nOverview\n=========\n\nThis project contains the commands which create direction vectors for several brain regions including the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain.\n\nDirection vectors are 3D unit vectors associated to voxels of a brain region.\nThey represent the directions of the fiber tracts and their streamlines are assumed to cross transversely layers in laminar brain regions.\n\nDirection vectors are used in placement-algorithm to set cells orientations.\n\nDirection vectors are also used to compute placement hints and split layer 2/3 of the AIBS mouse isocortex.\n\nAfter installation, you can display the available command lines with the following ``bash`` command:\n\n.. code-block:: bash\n\n    atlas-direction-vectors --help\n\nInstallation\n============\n\n.. code-block:: bash\n\n    pip install atlas-direction-vectors\n\nExamples\n========\n\nDirection Vectors\n-----------------\n\nGet the required input files:\n\n.. code-block:: bash\n\n   mkdir -p data/ccfv3\n\n   # hierarchy file:\n   curl -o data/1.json http://api.brain-map.org/api/v2/structure_graph_download/1.json\n\n   # CCFv3 annotation volume:\n   curl -o data/ccfv3/annotation_25.nrrd http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_25.nrrd\n\nRun the code (note, depending on the resolution of the volume, this may require significant amounts of available RAM):\n\n.. code-block:: bash\n\n    atlas-direction-vectors direction-vectors           \\\n        isocortex                                       \\\n        --hierarchy-path data/1.json                    \\\n        --annotation-path data/ccfv3/annotation_25.nrrd \\\n        --algorithm shading-blur-gradient               \\\n        --output-path data/ccfv3/direction_vectors.nrrd\n\nFor the placeholder orientations, one can compute the vectors for a particular\nregion with:\n\n.. code-block:: bash\n\n    atlas-direction-vectors direction-vectors           \\\n    from-center                                         \\\n        --region SSp                                    \\\n        --hierarchy-path data/1.json                    \\\n        --annotation-path data/ccfv3/annotation_25.nrrd \\\n        --output-path placeholder-direction_vectors.nrrd\n\nInstructions for developers\n===========================\n\nRun the following commands before submitting your code for review:\n\n.. code-block:: bash\n\n    cd atlas-direction-vectors\n    isort -l 100 --profile black atlas_direction_vectors tests setup.py\n    black -l 100 atlas_direction_vectors tests setup.py\n\nThese formatting operations will help you pass the linting check `testenv:lint` defined in `tox.ini`.\n\nCitation\n========\n\nWhen you use this software, we kindly ask you to cite the following DOI:\n\n.. image:: https://zenodo.org/badge/451806460.svg\n   :target: https://zenodo.org/badge/latestdoi/451806460\n\nAcknowledgements\n================\n\nThe development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.\n\nFor license and authors, see LICENSE.txt and AUTHORS.txt respectively.\n\nCopyright © 2022-2024 Blue Brain Project/EPFL\n\n.. substitutions\n\n.. |banner| image:: doc/source/static/atlas-direction-vectors.jpg\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fatlas-direction-vectors","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fatlas-direction-vectors","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fatlas-direction-vectors/lists"}