{"id":20956551,"url":"https://github.com/bluebrain/morphio","last_synced_at":"2025-03-01T22:47:38.409Z","repository":{"id":24316031,"uuid":"97694591","full_name":"BlueBrain/MorphIO","owner":"BlueBrain","description":"A python and C++ library for reading and writing neuronal morphologies","archived":false,"fork":false,"pushed_at":"2024-12-03T09:55:09.000Z","size":7959,"stargazers_count":27,"open_issues_count":41,"forks_count":24,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-02-15T20:14:20.978Z","etag":null,"topics":["glia","mitochondria","morphology","neuron","neurons","python","reticulum"],"latest_commit_sha":null,"homepage":"https://morphio.readthedocs.io","language":"C++","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.md","contributing":"CONTRIBUTING.md","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":"2017-07-19T08:50:52.000Z","updated_at":"2024-12-03T09:55:12.000Z","dependencies_parsed_at":"2024-01-11T12:03:42.848Z","dependency_job_id":"23ee9339-9627-46ab-93ed-8af4e56fc80c","html_url":"https://github.com/BlueBrain/MorphIO","commit_stats":{"total_commits":757,"total_committers":44,"mean_commits":"17.204545454545453","dds":0.6988110964332893,"last_synced_commit":"bdcea23bce365549deaa77e6dbfc66bacb6272c2"},"previous_names":[],"tags_count":58,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FMorphIO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FMorphIO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FMorphIO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FMorphIO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/MorphIO/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240236354,"owners_count":19769579,"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":["glia","mitochondria","morphology","neuron","neurons","python","reticulum"],"created_at":"2024-11-19T01:26:39.438Z","updated_at":"2025-03-01T22:47:38.402Z","avatar_url":"https://github.com/BlueBrain.png","language":"C++","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/MorphIO\n\n.. image:: doc/source/logo/BBP-MorphIO.jpg\n\n\n|license| |docs|\n\nMorphIO\n=======\n\nDocumentation\n-------------\n\nMorphIO documentation is built and hosted on `readthedocs \u003chttp://morphio.readthedocs.org/\u003e`_.\n\n* `latest snapshot \u003chttp://morphio.readthedocs.org/en/latest/\u003e`_\n* `latest release \u003chttp://morphio.readthedocs.org/en/stable/\u003e`_\n\nIntroduction\n------------\n\nMorphIO is a library for reading and writing neuron morphology files. It supports the following\nformats:\n\n* SWC\n* ASC (aka. neurolucida)\n* H5 v1\n* H5 v2 is not supported anymore, see `H5v2`_\n\nIt provides 3 C++ classes that are the starting point of every morphology analysis:\n\n* ``Soma``: contains the information related to the soma.\n\n* ``Section``: a section is the succession of points between two bifurcations. To the bare minimum\n  the ``Section`` object will contain the section type, the position and diameter of each point.\n\n* ``Morphology``: the morphology object contains general information about the loaded cell\n  but also provides accessors to the different sections.\n\nOne important concept is that MorphIO is split into a *read-only* part and a *read/write* one.\n\n\nH5v2\n====\n\nStarting at version 2.6.0, the file format ``h5v2`` is no longer supported. If you have\nmorphologies in this format, you can convert them to h5v1 with:\n\n.. code-block:: bash\n\n   pip install \"morphio\u003c2.6\" \"morph-tool==2.3.0\"\n\nand then:\n\n.. code-block:: bash\n\n   # single file, OUTPUT must end with `.h5`\n   morph-tool convert file INPUTFILE OUTPUT\n   # bulk conversion\n   morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR\n\n\nContributing\n============\nIf you want to improve the project or you see any issue, every contribution is welcome.\nPlease check the `contribution guidelines \u003chttps://github.com/BlueBrain/morphio/blob/master/CONTRIBUTING.md\u003e`_ for more\ninformation.\n\nAcknowledgements\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\nThis research was supported by the EBRAINS research infrastructure, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).\n\nLicense\n=======\nMorphIO is licensed under the terms of the Apache License 2.0.\nSee LICENSE.txt for further details.\n\nCopyright (c) 2013-2024 Blue Brain Project/EPFL\n\n.. |license| image:: https://img.shields.io/pypi/l/morphio\n                :target: https://github.com/BlueBrain/morphio/blob/master/COPYING.LESSER\n\n.. |docs| image:: https://readthedocs.org/projects/morphio/badge/?version=latest\n             :target: https://morphio.readthedocs.io/\n             :alt: documentation status\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fmorphio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fmorphio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fmorphio/lists"}