SpatialData: an open and universal framework for processing spatial omics data.

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: load data from common spatial omics technologies into spatialdata.
• spatialdata-plot: Static plotting library for spatialdata.
• napari-spatialdata: napari plugin for interactive exploration and annotation of spatial data.

spatialdata is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation 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 specification.

Getting started

Please refer to the documentation. In particular:

• API documentation.
• Design doc (includes the roadmap).
• Example notebooks.

Another useful resource to get started is the source code of the spatialdata-io package, which shows example of how to read data from common technologies.

Installation

Check out the docs for more complete installation instructions. To get started with the "batteries included" installation, you can install via pip:

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.

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 (public or 1 to 1).
• Forum post in the scverse discourse forum.
• Bug report/feature request via the GitHub issue tracker.
• Zoom call as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, schedule here.

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.

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