spatialdata-io 0.0.5

SpatialData IO for common techs

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:

• NanoString CosMx
• MCMICRO (output data)
• Steinbock (output data)
• 10x Genomics Visium
• 10x Genomics Xenium
• Curio Seeker
• Vizgen MERSCOPE (MERFISH)

Coming soon:

• Spatial Genomics seqFISH
• Akoya PhenoCycler (formerly CODEX)

Also coming soon:

• Common image converters: .jpg <> .zarr

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.

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