Welcome to METASPACE Converter’s documentation!

Python package to download and convert datasets from the METASPACE knowledge base to common formats for single-cell and spatial omics analysis. Datasets can be directly downloaded to AnnData and SpatialData objects.

AnnData is the underlying data format of many packages of the scverse such as ScanPy for single-cell data analysis and SquidPy for spatial omics analysis.

Another supported format that is part of the scverse is SpatialData for storing, aligning, and processing spatial omics data. This enables users to easily align and integrate METASPACE datasets to other spatial omics modalities.

The METASPACE-converter package uses the METASPACE python client to download datasets from METASPACE. If you also need to upload or modify datasets on METASPACE, please check the Python client documentation.

If you encounter bugs or have suggestions for new features, please open an issue on GitHub.

Installation

You can install the package via pip:

pip install metaspace-converter

Contents:

• API
  • metaspace_converter
  • metaspace_converter.colocalization
• Examples
  • Plain AnnData with ScanPy
  • SquidPy
  • Convert AnnData objects to ion image arrays
  • SpatialData
  • Colocalization Analysis

License

Unless specified otherwise source code in file headers or LICENSE files present in subdirectories, all files of this package are licensed under the Apache 2.0 license.