{"id":45836329,"url":"https://github.com/cgk-laboratory/pycroglia","last_synced_at":"2026-02-26T23:04:33.001Z","repository":{"id":305585558,"uuid":"997687405","full_name":"CGK-Laboratory/pycroglia","owner":"CGK-Laboratory","description":"A Python-based toolkit for quantitative 3D microglia morphology analysis","archived":false,"fork":false,"pushed_at":"2026-01-31T23:26:08.000Z","size":66753,"stargazers_count":2,"open_issues_count":15,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-02-01T08:59:49.845Z","etag":null,"topics":["cell-biology","image-processing","python"],"latest_commit_sha":null,"homepage":"https://cgk-laboratory.github.io/pycroglia/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CGK-Laboratory.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/CONTRIBUTING.md","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":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-06-07T01:05:07.000Z","updated_at":"2026-01-19T23:02:59.000Z","dependencies_parsed_at":"2025-10-07T03:34:49.184Z","dependency_job_id":null,"html_url":"https://github.com/CGK-Laboratory/pycroglia","commit_stats":null,"previous_names":["cgk-laboratory/pycroglia"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/CGK-Laboratory/pycroglia","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CGK-Laboratory%2Fpycroglia","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CGK-Laboratory%2Fpycroglia/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CGK-Laboratory%2Fpycroglia/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CGK-Laboratory%2Fpycroglia/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CGK-Laboratory","download_url":"https://codeload.github.com/CGK-Laboratory/pycroglia/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CGK-Laboratory%2Fpycroglia/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29876371,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-26T22:37:10.609Z","status":"ssl_error","status_checked_at":"2026-02-26T22:37:09.019Z","response_time":89,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["cell-biology","image-processing","python"],"created_at":"2026-02-26T23:04:30.922Z","updated_at":"2026-02-26T23:04:32.989Z","avatar_url":"https://github.com/CGK-Laboratory.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Pycroglia Banner](images/banner.png)\n\n# Pycroglia\n\n**A Python-based toolkit for quantitative 3D microglia morphology analysis**\n\nPycroglia is a modern, open-source port of **CellSelect-3DMorph**, a\nMATLAB-based tool originally designed to isolate and analyze cell\nmorphology from 3D fluorescence microscopy images.  By reconstructing\nindividual cells voxel by voxel, Pycroglia enables researchers to\nextract quantitative morphological descriptors such as **cell\nvolume**, **territorial volume**, **ramification index**, **branch\nlength**, **number of branches**, and **endpoints**, among others.  It\nbuilds upon the logic of the original MATLAB scripts but introduces a\nrobust and extensible Python architecture, supporting both GUI and\nlibrary modes for interactive and automated workflows.\n\n---\n\n## Installation and Usage\nPycroglia is available on [PyPI](https://pypi.org/project/pycroglia/)\nand can be installed or executed using\n[uv](https://github.com/astral-sh/uv) or the standard `pip` tool.\n\n### Prerequisites\n\n* [uv](https://docs.astral.sh/uv/getting-started/installation/) (Recommended): \n* Python 3.10 or later\n\n\n### Option 1 — Install with pip\n\nYou can install Pycroglia using pip directly from PyPI:\n\n```bash\npip install pycroglia\n```\nand to run it \n\n```bash\npycroglia\n```\n\n### Option 2 — Install with uv\n\nIf you prefer to use `uv`, which provides faster and isolated package management:\n\n```bash\nuv pip install pycroglia\n```\nand to run it \n\n```bash\npycroglia\n```\n\n\n### Option 3 — Run directly (recommended)\n\nYou can run Pycroglia without installing it globally, using `uvx`:\n\n```bash\nuvx pycroglia\n```\nThis automatically downloads and runs the latest released version from PyPI in an isolated environment.\n\nYou can also specify a particular version:\n```bash\nuvx pycroglia==0.0.2\n```\n\n### Option 4 — From source\n\nIf you cloned the repository and want to run it locally:\n\n```bash\ngit clone https://github.com/CGK-Laboratory/pycroglia/pycroglia.git\ncd pycroglia\nuv run main.py\n```\nand for running the test suite\n\n```bash\nuv run pytest\n```\n\n#### Use Pycroglia from a Jupyter Notebook\n\nIf you want to work within a *Jupyter Notebook*, launch a notebook\nserver connected to the project’s virtual environment:\n\n```bash\nuv run --with jupyter jupyter lab\n```\n\n## Contributing\nIf you are interested in contributing to the project follow the following guidelines\n[CONTRIBUTING](https://github.com/CGK-Laboratory/pycroglia/blob/main/docs/CONTRIBUTING.md)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgk-laboratory%2Fpycroglia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcgk-laboratory%2Fpycroglia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgk-laboratory%2Fpycroglia/lists"}