ArticleNature communications2025
msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- MALDI mass spectrometry imaging across spatial scales in toxicology: tissue evidence, cellular heterogeneity, and emerging single-cell opportunities.Analytical and bioanalytical chemistry · 2026Review
- Visualizing the molecular landscape of skin: applications and perspectives of mass spectrometry imaging.Analytical and bioanalytical chemistry · 2026Review
- Computational Mass Spectrometry Imaging in the Era of AI.Chemical reviews · 2026Review
- Review
- Spatial metabolomics: design, pitfalls and data interpretation.The EMBO journal · 2026Article
- MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.Communications biology · 2026Article
- Review
- MALDI spatial proteomics: a mini review of approaches and techniques.Analytical methods : advancing methods and applications · 2026Review
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Spatial biology using single-cell mass spectrometry imaging and integrated microscopy.Nature communications · 2025Article
- Single-cell lipidomics: performance evaluation across four liquid chromatography mass spectrometry (LC-MS) systems.The Analyst · 2025Article
- Neutrophils take their PICk to promote breast cancer.Nature cancer · 2025Article
- msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis.Nature communications · 2025Article
- A sulfatide-centered ultra-high-resolution magnetic resonance MALDI imaging benchmark dataset for MS1-based lipid annotation tools.GigaScience · 2025Article
Corrections and comments
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Authors and funding
22 authors.
Funding
Abstract
Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and microscopy holds potential for understanding pathological mechanisms by mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing software solutions for MALDI MSI data analysis are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high-throughput analysis to generate impactful biological discoveries. Here, we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multimodal imaging data. msiFlow integrates all necessary steps from raw data import to analytical visualisation along with state-of-the-art and self-developed algorithms into automated workflows. Using msiFlow, we unravel the molecular heterogeneity of leukocytes in infected tissues by spatial regulation of ether-linked phospholipids containing arachidonic acid. We anticipate that msiFlow will facilitate the broad applicability of MSI in multimodal imaging to uncover context-dependent cellular regulations in disease states.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.