Batch correction for large-scale mass spectrometry imaging experiments

Thomsen, A. A.; Jensen, O. N.

doi:10.64898/2026.01.30.702769

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bioRxiv · 10.64898/2026.01.30.702769

Batch correction for large-scale mass spectrometry imaging experiments

Thomsen, A. A.·Jensen, O. N.

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Abstract

We assess batch correction methods for MALDI mass spectrometry imaging experiments. ComBAT reduced batch-related technical variance, maintained biological variation, and improved the overall score by 19.4%. Availability and implementationMethods are available in R. comBAT is used through the "sva" package while Harmony, CCA, FastMNN are available in the "Seurat" package https://github.com/satijalab/seurat. scVI, scANVI are Scanorama are available in the Python programming language and through github: https://github.com/scverse/scvi-tools.

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Thomsen, A. A., Jensen, O. N.. 2026-02-02. Batch correction for large-scale mass spectrometry imaging experiments. https://doi.org/10.64898/2026.01.30.702769

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