msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 27, 2025

Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry (MALDI MSI) and microscopy holds potential for understanding pathological mechanisms mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing software solutions MALDI MSI data analysis are incomplete, require programming skills contain laborious manual steps, hindering broadly applicable, reproducible, high-throughput generate impactful biological discoveries. Here, we present msiFlow, an accessible open-source, platform-independent vendor-neutral end-to-end, high-throughput, transparent reproducible of multimodal data. msiFlow integrates all necessary steps raw import analytical visualisation along with state-of-the-art self-developed algorithms into automated workflows. Using unravel heterogeneity leukocytes in infected tissues spatial regulation ether-linked phospholipids containing arachidonic acid. We anticipate that will facilitate broad applicability uncover context-dependent cellular regulations disease states. This paper introduces open-source scalable end-to-end image analysis. authors explore tissues.

Language: Английский

Imaging and spatially resolved mass spectrometry applications in nephrology

Nature Reviews Nephrology, Journal Year: 2025, Volume and Issue: unknown

Published: March 27, 2025

Language: Английский