https://github.com/scverse/spatialdata
An open and interoperable data framework for spatial omics data
https://github.com/scverse/spatialdata
Last synced: 4 months ago
JSON representation
An open and interoperable data framework for spatial omics data
- Host: GitHub
- URL: https://github.com/scverse/spatialdata
- Owner: scverse
- License: bsd-3-clause
- Created: 2022-04-30T19:41:52.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-06-23T17:35:48.000Z (12 months ago)
- Last Synced: 2025-06-23T18:40:21.803Z (12 months ago)
- Language: Python
- Homepage: https://spatialdata.scverse.org/
- Size: 2.29 MB
- Stars: 289
- Watchers: 12
- Forks: 62
- Open Issues: 229
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
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README
# SpatialData: an open and universal framework for processing spatial omics data.
[![Tests][badge-tests]][link-tests]
[](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[](https://codecov.io/gh/scverse/spatialdata)
[](https://spatialdata.scverse.org/en/latest/)
[](https://zenodo.org/badge/latestdoi/487366481)
[](https://pepy.tech/project/spatialdata)
[](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
[](https://anaconda.org/conda-forge/spatialdata)
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/
SpatialData 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.
- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
[//]: # "numfocus-fiscal-sponsor-attribution"
spatialdata 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/).
If 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.
The spatialdata project also received support by the Chan Zuckerberg Initiative.
- **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.
- The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification.
## Getting started
Please refer to the [documentation][link-docs]. In particular:
- [API documentation][link-api].
- [Design doc][link-design-doc] (includes the roadmap).
- [Example notebooks][link-notebooks].
Another 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.
## Installation
Check 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:
```bash
pip install "spatialdata[extra]"
```
~~or via conda:~~
Update 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`.
```bash
mamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot
```
## Limitations
- 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.
## Contact
To get involved in the discussion, or if you need help to get started, you are welcome to use the following options.
- Chat via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1).
- Forum post in the [scverse discourse forum](https://discourse.scverse.org/).
- Bug report/feature request via the [GitHub issue tracker][issue-tracker].
- Zoom call 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) **<--- new link!**.
Finally, especially relevant for for developers that are building a library upon `spatialdata`, please follow this channel for:
- Announcements on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements).
## Citation
Marconato, 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
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/scverse/spatialdata/issues
[design doc]: https://scverse-spatialdata.readthedocs.io/en/stable/design_doc.html
[link-docs]: https://spatialdata.scverse.org/en/stable/
[link-api]: https://spatialdata.scverse.org/en/stable/api.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[badge-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml/badge.svg
[link-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml