Mass Spectrometry Imaging Python Packages

divik

Divisive Intelligent K-Means algorithm (DiviK) for joint feature selection and clustering of heavily multidimensional data.

thyra

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

imzdesk

WSI-MSI Workbench

m2aia

pyM²aia is a Python package for memory-efficient access and processing of mass spectrometry image data. The I/O functionality is derived from the interactive desktop application M²aia. Special features are the batch generator utilities for deep learning applications.

pimz

This framework allows to perform scRNA-seq-like analyses of imaging mass-spectrometry data. Check out the example jupyter-notebook in examples/