{"id":20956454,"url":"https://github.com/bluebrain/atlas-enhancement","last_synced_at":"2025-05-14T05:31:49.858Z","repository":{"id":224937338,"uuid":"753641843","full_name":"BlueBrain/atlas-enhancement","owner":"BlueBrain","description":"Tools to generate flatmaps of brain atlases \u0026 code to add barrel and barrel column annotations to Allen Mouse CCFv3","archived":false,"fork":false,"pushed_at":"2024-07-04T15:31:04.000Z","size":17297,"stargazers_count":2,"open_issues_count":1,"forks_count":3,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-11-13T01:03:04.622Z","etag":null,"topics":["neuroinformatics","neuroscience"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2024-02-06T14:22:49.000Z","updated_at":"2024-07-01T10:03:13.000Z","dependencies_parsed_at":"2024-04-30T21:41:57.264Z","dependency_job_id":"d10ad0f5-d952-4561-b906-d5c6aad3b4ea","html_url":"https://github.com/BlueBrain/atlas-enhancement","commit_stats":null,"previous_names":["bluebrain/atlas-enhancement"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-enhancement","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-enhancement/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-enhancement/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fatlas-enhancement/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/atlas-enhancement/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225277056,"owners_count":17448613,"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":["neuroinformatics","neuroscience"],"created_at":"2024-11-19T01:26:03.293Z","updated_at":"2025-05-14T05:31:49.828Z","avatar_url":"https://github.com/BlueBrain.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003e [!WARNING]\n\u003e The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.\n\u003e Future development will take place at: https://github.com/openbraininstitute/atlas-enhancement\n\n# Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations\n\nThis code accompanies the manuscript \"Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations\" by S. Bolaños-Puchet, A. Teska, et al.\n\nPreprint containing full methods and applications availble on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.08.24.554204).\n\nAccompanying data available on [Zenodo](https://zenodo.org/doi/10.5281/zenodo.8165004).\n\n\n## Generation of depth and orientation fields\n\nTo generate depth and orientation fields, please refer to the documentation of the following repositories:\n\n* [regiodesics](https://github.com/BlueBrain/regiodesics)\n* [atlas-direction-vectors](https://github.com/BlueBrain/atlas-direction-vectors)\n* [atlas-placement-hints](https://github.com/BlueBrain/atlas-placement-hints/)\n\n\n## Flatmapping\n\nComplete workflow to generate flatmaps and perform flatmap-based applications, including visualizing 3D datasets in flat space. For more details, please look at the [README](flatmap/README.md) under `flatmap`.\n\n\n## Annotation of barrels and barrel columns \n\nCode needed to add barrel cortex annotations to the CCFv3 Allen Atlas at 10 $\\mu m$ resolution. For more details, please look at the [README](barrel-annotations/README.md) under `barrel-annotations`.\n\n\n## Citation\n\nIf you use the ``atlas-enhancement`` code or method for your research, we ask you to [cite](https://www.biorxiv.org/content/10.1101/2023.08.24.554204):\n\n\u003e Bolaños-Puchet S., Teska A., et al. (2024). Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations. bioRxiv. DOI: 10.1101/2023.08.24.554204\n\n\n## Funding \u0026 Acknowledgments\n\nThis project/research 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\nCopyright (c) 2020-2024 Blue Brain Project/EPFL.\n\n\n## License\n\nThis work is licensed under the Apache License, Version 2.0.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fatlas-enhancement","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fatlas-enhancement","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fatlas-enhancement/lists"}