spatialdata-io: convenient readers for loading common formats into SpatialData

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spatialdata-io: convenient readers for loading common formats into SpatialData#

Tests Documentation DOI

This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:

  • 10x Genomics Visium

  • 10x Genomics Visium HD

  • 10x Genomics Xenium

  • Akoya PhenoCycler (formerly CODEX)

  • Curio Seeker

  • DBiT-seq

  • MCMICRO (output data)

  • NanoString CosMx

  • Steinbock (output data)

  • STOmics Stereo-seq

  • Vizgen MERSCOPE (MERFISH)

Getting started#

Please refer to the documentation. In particular, the

Installation#

You need to have Python 3.8 or newer installed on your system. If you don’t have Python installed, we recommend installing Miniconda.

There are several alternative options to install spatialdata-io:

  1. Install the latest release of spatialdata-io from PyPI:

pip install spatialdata-io
  1. Install the latest development version:

pip install git+https://github.com/scverse/spatialdata-io.git@main

Contact#

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Readers from third-party libraries#

Technologies that can be read into SpatialData objects using third-party libraries:

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