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)
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:
Install the latest release of
spatialdata-io
from PyPI:
pip install spatialdata-io
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