Treffer: pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning.

Summary Python is the most commonly used language for deep learning (DL). Existing Python packages for mass spectrometry imaging (MSI) data are not optimized for DL tasks. We, therefore, introduce pyM²aia, a Python package for MSI data analysis with a focus on memory-efficient handling, processing and convenient data-access for DL applications. pyM²aia provides interfaces to its parent application M²aia, which offers interactive capabilities for exploring and annotating MSI data in imzML format. pyM²aia utilizes the image input and output routines, data formats, and processing functions of M²aia, ensures data interchangeability, and enables the writing of readable and easy-to-maintain DL pipelines by providing batch generators for typical MSI data access strategies. We showcase the package in several examples, including imzML metadata parsing, signal processing, ion-image generation, and, in particular, DL model training and inference for spectrum-wise approaches, ion-image-based approaches, and approaches that use spectral and spatial information simultaneously. Availability and implementation Python package, code and examples are available at (https://m2aia.github.io/m2aia) [ABSTRACT FROM AUTHOR]

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