{"id":34091536,"url":"https://github.com/goehringlab/saibr_python","last_synced_at":"2026-06-09T09:31:40.816Z","repository":{"id":65442820,"uuid":"588706167","full_name":"goehringlab/saibr_python","owner":"goehringlab","description":"Python implementation of SAIBR: a tool for performing spectral autofluorescence correction on biological images","archived":false,"fork":false,"pushed_at":"2023-11-17T15:29:24.000Z","size":79743,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-16T18:16:47.126Z","etag":null,"topics":["image-processing","python"],"latest_commit_sha":null,"homepage":"https://saibr.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/goehringlab.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":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-01-13T19:37:17.000Z","updated_at":"2024-03-06T08:24:44.000Z","dependencies_parsed_at":"2023-02-13T02:31:34.768Z","dependency_job_id":null,"html_url":"https://github.com/goehringlab/saibr_python","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/goehringlab/saibr_python","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/goehringlab%2Fsaibr_python","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/goehringlab%2Fsaibr_python/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/goehringlab%2Fsaibr_python/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/goehringlab%2Fsaibr_python/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/goehringlab","download_url":"https://codeload.github.com/goehringlab/saibr_python/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/goehringlab%2Fsaibr_python/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34101065,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-09T02:00:06.510Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["image-processing","python"],"created_at":"2025-12-14T14:44:39.058Z","updated_at":"2026-06-09T09:31:40.811Z","avatar_url":"https://github.com/goehringlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SAIBR (python implementation)\n\n[![CC BY 4.0][cc-by-shield]][cc-by]\n[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white)](https://github.com/pre-commit/pre-commit)\n[![Tests](https://github.com/goehringlab/saibr_python/actions/workflows/test.yaml/badge.svg)](https://github.com/goehringlab/saibr_python/actions/workflows/test.yaml)\n[![PyPi version](https://badgen.net/pypi/v/saibr/)](https://pypi.org/project/saibr)\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/goehringlab/saibr_python/HEAD?filepath=%2Fscripts/SAIBRdemonstration.ipynb)\n[![Documentation Status](https://readthedocs.org/projects/saibr/badge/?version=latest)](https://saibr.readthedocs.io/en/latest/?badge=latest)\n\n\nPython implementation of SAIBR: a simple, platform independent protocol for spectral autofluorescence correction\n\n[Paper](https://journals.biologists.com/dev/article/149/14/dev200545/276004/SAIBR-a-simple-platform-independent-method-for)\n\n[FIJI plugin](https://github.com/goehringlab/saibr_fiji_plugin)\n\n\n## Tutorial notebook\n\nAs a first step, I would recommend checking out the [tutorial notebook](https://nbviewer.org/github/goehringlab/saibr_python/blob/master/scripts/SAIBRdemonstration.ipynb). This can be run in the cloud using Binder (please note that it may take several minutes to open the notebook):\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/goehringlab/saibr_python/HEAD?filepath=%2Fscripts/SAIBRdemonstration.ipynb)\n\nTo run locally, download the code and install the relevant requirements (requirements.txt) in a virtual environment.\n\n\n## Install instructions\n\nTo explore further and incorporate into your own analysis pipelines, you can install the package from PyPI using pip:\n\n    pip install saibr\n\nIf you want to make changes to the code you can download/clone this folder, navigate to it, and run:\n\n    pip install -e .[dev]\n\n\n## Citation\n\nIf you use this method as part of a publication, please cite the following reference: \n\nNelio T. L. Rodrigues, Tom Bland, Joana Borrego-Pinto, KangBo Ng, Nisha Hirani, Ying Gu, Sherman Foo, Nathan W. Goehring; SAIBR: a simple, platform-independent method for spectral autofluorescence correction. Development 15 July 2022; 149 (14): dev200545. doi: https://doi.org/10.1242/dev.200545\n\n## License\n\nThis work is licensed under a\n[Creative Commons Attribution 4.0 International License][cc-by].\n\n[![CC BY 4.0][cc-by-image]][cc-by]\n\n[cc-by]: http://creativecommons.org/licenses/by/4.0/\n[cc-by-image]: https://i.creativecommons.org/l/by/4.0/88x31.png\n[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgoehringlab%2Fsaibr_python","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgoehringlab%2Fsaibr_python","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgoehringlab%2Fsaibr_python/lists"}