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

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

• API documentation.

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

2. 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:

• METASPACE (MALDI, ...): metaspace-converter
• PhenoCycler: SOPA
• MACSima: SOPA
• Hyperion (Imaging Mass Cytometry): SOPA

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