{"id":13752038,"url":"https://github.com/scverse/spatialdata","last_synced_at":"2026-02-11T17:14:04.323Z","repository":{"id":40709335,"uuid":"487366481","full_name":"scverse/spatialdata","owner":"scverse","description":"An open and interoperable data framework for spatial omics data","archived":false,"fork":false,"pushed_at":"2025-06-23T17:35:48.000Z","size":2396,"stargazers_count":289,"open_issues_count":229,"forks_count":62,"subscribers_count":12,"default_branch":"main","last_synced_at":"2025-06-23T18:40:21.803Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://spatialdata.scverse.org/","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/scverse.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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}},"created_at":"2022-04-30T19:41:52.000Z","updated_at":"2025-06-19T09:57:07.000Z","dependencies_parsed_at":"2023-11-19T01:28:05.208Z","dependency_job_id":"b22ba1f4-16a9-47ac-815c-8ac71c8d65ca","html_url":"https://github.com/scverse/spatialdata","commit_stats":null,"previous_names":[],"tags_count":42,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/spatialdata","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fspatialdata","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fspatialdata/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fspatialdata/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fspatialdata/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/spatialdata/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fspatialdata/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"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":[],"created_at":"2024-08-03T09:00:58.470Z","updated_at":"2026-02-01T14:02:49.572Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)\n\n# SpatialData: an open and universal framework for processing spatial omics data.\n\n[![Tests][badge-tests]][link-tests]\n[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)\n[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)\n[![documentation badge](https://readthedocs.org/projects/scverse-spatialdata/badge/?version=latest)](https://spatialdata.scverse.org/en/latest/)\n[![DOI](https://zenodo.org/badge/487366481.svg)](https://zenodo.org/badge/latestdoi/487366481)\n[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)\n[![Release](https://github.com/scverse/spatialdata/actions/workflows/release.yaml/badge.svg?event=release)](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)\n[![Documentation][badge-pypi]][link-pypi]\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/spatialdata/badges/version.svg)](https://anaconda.org/conda-forge/spatialdata)\n\n[badge-pypi]: https://badge.fury.io/py/spatialdata.svg\n[link-pypi]: https://pypi.org/project/spatialdata/\n\nSpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.\n\n- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.\n- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.\n- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.\n\n[//]: # \"numfocus-fiscal-sponsor-attribution\"\n\nspatialdata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\nThe spatialdata project also received support by the Chan Zuckerberg Initiative.\n\n\u003cdiv align=\"center\"\u003e\n  \u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n    \u003cimg height=\"60px\"\n         src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n         align=\"center\"\u003e\n  \u003c/a\u003e\n\u003c/div\u003e\n\u003cbr\u003e\n\n![SpatialDataOverview](https://github.com/scverse/spatialdata/assets/1120672/cb91071f-12a7-4b8e-9430-2b3a0f65e52f)\n\n- **The library is currently under review.** We expect there to be changes as the community provides feedback. We have an announcement channel for communicating these changes, please see the contact section below.\n- The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification.\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular:\n\n- [API documentation][link-api].\n- [Design doc][link-design-doc] (includes the roadmap).\n- [Example notebooks][link-notebooks].\n\nAnother useful resource to get started is the source code of the [`spatialdata-io`](https://github.com/scverse/spatialdata-io) package, which shows example of how to read data from common technologies.\n\n## Installation\n\nCheck out the docs for more complete [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html). To get started with the \"batteries included\" installation, you can install via pip:\n\n```bash\npip install \"spatialdata[extra]\"\n```\n\n~~or via conda:~~\nUpdate Feb 2025: `spatialdata` cannot be currently be installed via `conda` because some dependencies of our dependencies are not updated in `conda-forge` and we are still waiting for an update. Please install from `pip`; the latest versions of the `spatialdata` libraries are always available via `PyPI`.\n\n```bash\nmamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot\n```\n\n## Limitations\n\n- Code only manually tested for Windows machines. Currently the framework is being developed using Linux, macOS and Windows machines, but it is automatically tested only for Linux and macOS machines.\n\n## Contact\n\nTo get involved in the discussion, or if you need help to get started, you are welcome to use the following options.\n\n- \u003cins\u003eChat\u003c/ins\u003e via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1).\n- \u003cins\u003eForum post\u003c/ins\u003e in the [scverse discourse forum](https://discourse.scverse.org/).\n- \u003cins\u003eBug report/feature request\u003c/ins\u003e via the [GitHub issue tracker][issue-tracker].\n- \u003cins\u003eZoom call\u003c/ins\u003e as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, [schedule here](https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/spatialdata.20meetings/near/540899686) **\u003c--- new link!**.\n\nFinally, especially relevant for for developers that are building a library upon `spatialdata`, please follow this channel for:\n\n- \u003cins\u003eAnnouncements\u003c/ins\u003e on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements).\n\n## Citation\n\nMarconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x\n\n\u003c!-- Links --\u003e\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/scverse/spatialdata/issues\n[design doc]: https://scverse-spatialdata.readthedocs.io/en/stable/design_doc.html\n[link-docs]: https://spatialdata.scverse.org/en/stable/\n[link-api]: https://spatialdata.scverse.org/en/stable/api.html\n[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html\n[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html\n[badge-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml/badge.svg\n[link-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fspatialdata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fspatialdata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fspatialdata/lists"}