{"id":20956456,"url":"https://github.com/bluebrain/morphoclass","last_synced_at":"2025-05-14T05:31:47.980Z","repository":{"id":37905030,"uuid":"476637222","full_name":"BlueBrain/morphoclass","owner":"BlueBrain","description":"Neuronal morphology preparation and classification using Machine 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alt=\"MorphoClass Banner\" src=\"docs/source/logo/morphoclass-banner.jpg\"/\u003e\n\n# Morphology-Classification\nMorphoClass is a toolbox for neuronal morphologies processing and\nclassification using machine learning.\n\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eDocumentation\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://morphoclass.readthedocs.io/en/latest/\"\u003e\n                \u003cimg src=\"https://readthedocs.org/projects/morphoclass/badge/?version=latest\" alt=\"Docs\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eLicense\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://github.com/BlueBrain/morphoclass/blob/master/LICENSE.txt\"\u003e\n                \u003cimg src=\"https://img.shields.io/github/license/BlueBrain/morphoclass\" alt=\"License\" /\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eStatic Typing\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"http://mypy-lang.org/\"\u003e\n                \u003cimg src=\"http://www.mypy-lang.org/static/mypy_badge.svg\" alt=\"Mypy\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eCode Style\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://github.com/psf/black\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/code%20style-black-000000.svg\" alt=\"Black\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://pycqa.github.io/isort/\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat\u0026labelColor=ef8336\" alt=\"Isort\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://flake8.pycqa.org/\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/PEP8-flake8-informational\" alt=\"Pydocstyle\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eCI\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://github.com/BlueBrain/morphoclass/actions/workflows/ci.yaml?query=branch:main\"\u003e\n                \u003cimg src=\"https://img.shields.io/github/workflow/status/BlueBrain/morphoclass/CI/main\" alt=\"CI Status\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n\u003c/table\u003e\n\n\n# Installation\nClone the repository and set up the virtual environment\n```sh\ngit clone git@github.com:BlueBrain/morphoclass.git\ncd morphoclass\npython --version  # should be 3.8\npython -m venv venv\n. venv/bin/activate\n```\n\nInstall `morphoclass`\n```sh\n./install.sh\n```\n\nOpen the file `docs/build/html/index.html` to view the documentation.\n\n# Examples\nMorphoClass functionalities can be accessed using either a command line\ninterface or by importing `morphoclass` as a Python module and using it as a\nlibrary.\n\n## Command-Line Interface\nBy installing MorphoClass, we get access to a command line interface with a\nmain entrypoint `morphoclass` and various sub-commands.\n```sh\nmorphoclass --help\n```\n```\nUsage: morphoclass [OPTIONS] COMMAND [ARGS]...\n\n  Welcome to the command line application for morphoclass.\n\n  All functionality is provided through respective sub-commands. To learn more\n  about their functionality call the corresponding sub-command with the --help\n  flag to see a detailed description.\n\nOptions:\n  ...\n\nCommands:\n  ...\n```\n\nFor instance, to train a model for classifying neuronal morphologies, we can\ncheck the help of the corresponding sub-command.\n```sh\nmorphoclass train --help\n```\n```\nUsage: morphoclass train [OPTIONS]\n\n  Train a morphology classification model.\n\nOptions:\n  ...\n```\n\n## Python Interface\nMorphoClass is a pure Python package, and can be used as any other module once\nit is installed.\n\nFor instance, we can load a PersLay-based model for morphology classification\nand check its documentation as follows.\n```py\n\u003e\u003e\u003e from morphoclass.models.coriander_net import CorianderNet\n\u003e\u003e\u003e help(CorianderNet)\n```\n```\nHelp on class CorianderNet in module morphoclass.models.coriander_net:\n\nclass CorianderNet(torch.nn.modules.module.Module)\n |  CorianderNet(n_classes=4, n_features=64, dropout=False)\n |\n |  A PersLay-based neural network for neuron m-type classification.\n |\n |  Parameters\n |  ----------\n ...\n```\n\n# Documentation\nFor more examples and details on the installation, development setup, docker,\nthe command line interface, and the python API please see the extended\ndocumentation on https://morphoclass.readthedocs.io\n\n# Funding \u0026 Acknowledgment\nThe development of this software was supported by funding to the Blue Brain\nProject, a research center of the École polytechnique fédérale de Lausanne\n(EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes\nof Technology.\n\nCopyright © 2022-2022 Blue Brain Project/EPFL\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fmorphoclass","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fmorphoclass","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fmorphoclass/lists"}