Software

Tools I build to bring mass spectrometry imaging into the spatial omics ecosystem, and the open-source projects I contribute to.

Projects

M4i-Imaging-Mass-Spectrometry/thyra

Python library that converts mass spectrometry imaging data (imzML and Bruker) into the SpatialData/Zarr format, so MSI can be analysed alongside other spatial omics data.

pip install thyra

Python · MIT license · Author and maintainer

MALDI-MSI and Xenium overlay

M4i-Imaging-Mass-Spectrometry/MALDI-MSI---Spatial-Transcriptomics-Overlay

Prepares 10x Xenium spatial transcriptomics output (expression, clusters and cell outlines) for overlay with MALDI-MSI. The code behind "One section, two worlds" in Scientific Reports.

Python · Author

GitHub
Paper

Contributions

zarr-python zarr-developers

Chunked, compressed N-dimensional arrays for Python.
- Merged Retry the LocalStore rename when the destination is busy
- Merged Fix an infinite loop when choosing shard chunks for 0-dimensional arrays
spatialdata scverse

An open and interoperable data framework for spatial omics data.
spatialdata-io scverse

Readers that load spatial omics technologies into SpatialData.
- In review Import the Xenium onboard analysis (clustering, PCA, UMAP, differential expression) into the table