Spatial data format.
Project description
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 spatialdata.
- The library is currently under review. We expect there to be changes as the community provides feedback.
- To get involved in the discussion, or if you need help to get started, you are welcome to join our
scverseZulip chat and our scverse discourse forum. - The SpatialData storage format is built on top of the OME-NGFF specification.
Getting started
Please refer to the documentation. In particular:
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]"
Contact
For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.
Citation
L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023. * = equal contribution
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