{"id":37085255,"url":"https://github.com/sanderslab/magellanmapper","last_synced_at":"2026-01-14T10:28:52.601Z","repository":{"id":37093247,"uuid":"243180375","full_name":"sanderslab/magellanmapper","owner":"sanderslab","description":"MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification","archived":false,"fork":false,"pushed_at":"2026-01-02T19:22:00.000Z","size":9054,"stargazers_count":22,"open_issues_count":32,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-05T05:08:58.671Z","etag":null,"topics":["3d-reconstruction","atlas","bioimage-analysis","cell-detection","gui","image-processing","image-registration","microscopy-image-analysis","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sanderslab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-02-26T05:55:15.000Z","updated_at":"2025-12-31T18:50:18.000Z","dependencies_parsed_at":"2025-12-13T08:04:40.372Z","dependency_job_id":null,"html_url":"https://github.com/sanderslab/magellanmapper","commit_stats":null,"previous_names":[],"tags_count":147,"template":false,"template_full_name":null,"purl":"pkg:github/sanderslab/magellanmapper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanderslab%2Fmagellanmapper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanderslab%2Fmagellanmapper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanderslab%2Fmagellanmapper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanderslab%2Fmagellanmapper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanderslab","download_url":"https://codeload.github.com/sanderslab/magellanmapper/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanderslab%2Fmagellanmapper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28417264,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T10:25:19.714Z","status":"ssl_error","status_checked_at":"2026-01-14T10:22:49.371Z","response_time":107,"last_error":"SSL_read: 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":["3d-reconstruction","atlas","bioimage-analysis","cell-detection","gui","image-processing","image-registration","microscopy-image-analysis","python"],"created_at":"2026-01-14T10:28:51.696Z","updated_at":"2026-01-14T10:28:52.596Z","avatar_url":"https://github.com/sanderslab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MagellanMapper\n\nMagellanMapper is a graphical imaging informatics suite for 3D reconstruction and automated analysis of whole specimens and atlases. Its design philosophy is to make the raw 3D images as accessible as possible, simplify annotation from nuclei to atlases, and scale from the laptop or desktop to the cloud in cross-platform environments.\n\n![ROI Editor and Atlas Editor screenshots](https://user-images.githubusercontent.com/1258953/195321971-955fc46a-f44d-4282-8c78-21708ebaeef1.png)\n\n\u003ca href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781073/\"\u003e\u003cimg align=\"right\" width=\"200\" src=\"https://user-images.githubusercontent.com/1258953/179440433-0326c4d5-9a9b-4bae-92c7-d09416375bc5.png\" title=\"Current Protocols cover image\"\u003e\u003c/a\u003e\n\n\n## Quick Reference\n\n- [Docs are now on ReadTheDocs!](https://magellanmapper.readthedocs.io/en/latest/)\n- **NEW**: [Vignette of pipelines](bin/sample_cmds_bash.ipynb)\n- [Installation](#quick-install) (more [details](docs/install.md))\n- [Intro to running MagellanMapper](#run-magellanmapper)\n- [Using the viewers](docs/viewers.md)\n- [Command-line interface](docs/cli.md)\n- [Configuration and settings](docs/settings.md)\n- [Publications](#related-publications-and-datasets)\n\n\n## Quick Install\n\nInstall MagellanMapper with its graphical interface and registration tools:\n\n```shell\npip install \"magellanmapper[gui,itk]\"\n```\n\nThen launch MagellanMapper:\n\n```shell\nmm\n```\n\n### Conda Install\n\nMagellanMapper can also be installed in [Conda](https://docs.conda.io/en/latest/miniconda.html):\n\n```shell\nconda env create -n mag -f https://raw.githubusercontent.com/sanderslab/magellanmapper/master/envs/environment_rel.yml\n```\n\nThen activate the environment (`mag`) and run MagellanMapper:\n\n```shell\nconda activate mag\nmm\n```\n\n### Pre-release\n\n*UPDATE*: As of MM v1.7-pre, Java/Bioformats and a custom Python repo are no longer required to import image files. TIF files can be imported directly into MM. To install the latest pre-release in regular or Conda environments, run:\n\n```shell\n pip install --pre \"magellanmapper[most]\"\n ```\n\n### Developer Install (ie \"the latest and greatest\")\n\nFor the latest updates and fixes, download from Git and install:\n\n```shell\ngit clone https://github.com/sanderslab/magellanmapper.git\nconda env create -n mag -f magellanmapper/environment.yml\nmm\n```\n\nOr for Pip, replace the `conda` line with:\n\n```shell\npip install -e \"magellanmapper[most]\"\n```\n\nSee the [install docs](docs/install.md) for more details and other install scenarios.\n\n## Using MagellanMapper\n\nMagellanMapper consists of a graphical user interface (GUI), command-line interface (CLI), and application programming interface (API) for Python programmatic access. See the [GUI docs](docs/viewers.md) for graphical usage and the [CLI docs](docs/cli.md) for scripting.\n\nFor automated tasks, see the [`sample_cmds_bash.ipynb`](bin/sample_cmds_bash.ipynb) Jupyter Notebook (or the older [`sample_cmds.sh`](bin/sample_cmds.sh) script) that shows examples of running the CLI and exploring images in the GUI. See ReadTheDocs for more details, including [viewer shortcuts](docs/viewers.md) and customizing [settings](docs/settings.md) for your image analysis.\n\nHave a question? Found a bug? Want a feature? Please [ask](https://github.com/sanderslab/magellanmapper/issues)!\n\n### Image file import\n\nMagellanMapper reads large images using on-the-fly loading to reduce memory requirements and load time. NumPy (`.npy`) is the default image format.\n\nLarge TIF files can also be opened. In the \"Import\" tab, you can select files, view and update metadata, and import these files. Proprietary microscopy formats such as CZI can separately converted to TIF in ImageJ/FIJI or the microscope's software. \n\nMedical imaging formats such as `.mha` (or `.mhd/.raw`) and `.nii` (or `.nii.gz`) can also be opened. \n\n### Sample 3D data\n\nTo try out functions with sample images, download any of these files:\n\n- [Sample region of nuclei at 4x (`sample_region.zip`)](https://github.com/sanderslab/magellanmapper/releases/download/v1.1.3/sample_region.zip)\n- [Sample downsampled tissue cleared whole brain (`sample_brain.zip`)](https://github.com/sanderslab/magellanmapper/releases/download/v1.1.3/sample_brain.zip)\n- [Allen Developing Mouse Brain Atlas E18.5 (`ADMBA-E18pt5.zip`)](https://github.com/sanderslab/magellanmapper/releases/download/v1.1.3/ADMBA-E18pt5.zip)\n\n## Related publications and datasets\n\n- For more information on the methods used for 3D atlas construction, please see: https://elifesciences.org/articles/61408\n- For step-by-step instructions on using v1.3.x of the software, please see: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpns.104 (now [open access on PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781073/)!); see [ReadTheDocs](https://magellanmapper.readthedocs.io/en/latest/) for ongoing updates\n- The 3D reconstructed versions of the Allen Developing Mouse Brain Atlas: https://search.kg.ebrains.eu/instances/Project/b8a8e2d3-4787-45f2-b010-589948c33f20\n- Sample wild-type whole mouse brains at age P0: https://search.kg.ebrains.eu/instances/Dataset/2423e103-35e9-40cf-ab0c-0e3d08d24d5a\n\nLicensed under the open-source [BSD-3 license](LICENSE.txt)\n\nAuthor: David Young, 2017, 2025\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsanderslab%2Fmagellanmapper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsanderslab%2Fmagellanmapper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsanderslab%2Fmagellanmapper/lists"}