ArticleGigaScience2025
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mass spectrometry-based human spatial omics: fundamentals, innovations, and applications.Journal of biomedical science · 2026Pooled it
- An Integrated Spatial Multi-Omics Workflow for Sequential RNA and Protein Profiling in FFPE Tumor Tissue.Cancer research communications · 2026Article
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026Review
- SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and visualization.GigaScience · 2026Article
- Research Progress on the Application of Mass Spectrometry Imaging Technology in Cerebral Disease.Life (Basel, Switzerland) · 2026Review
- Spatial multi-omics technologies in gastric cancer: applications and advances.Frontiers in immunology · 2026Review
- One section, two worlds: single-cell integration of MALDI-MSI and spatial transcriptomics on the same single tissue section.Scientific reports · 2025Article
- Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment.Nature communications · 2025Article
- Spatial Transcriptomics in Lung Cancer and Pulmonary Diseases: A Comprehensive Review.Cancers · 2025Review
- Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset.GigaScience · 2025Article
- Mechanisms and technologies in cancer epigenetics.Frontiers in oncology · 2024Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundTruly understanding the cancer biology of heterogeneous tumors in precision medicine requires capturing the complexities of multiple omics levels and the spatial heterogeneity of cancer tissue. Techniques like mass spectrometry imaging (MSI) and spatial transcriptomics (ST) achieve this by spatially detecting metabolites and RNA but are often applied to serial sections. To fully leverage the advantage of such multi-omics data, the individual measurements need to be integrated into 1 dataset.
resultsWe present the Multi-Omics Imaging Integration Toolset (MIIT), a Python framework for integrating spatially resolved multi-omics data. A key component of MIIT's integration is the registration of serial sections for which we developed a nonrigid registration algorithm, GreedyFHist. We validated GreedyFHist on 244 images from fresh-frozen serial sections, achieving state-of-the-art performance. As a proof of concept, we used MIIT to integrate ST and MSI data from prostate tissue samples and assessed the correlation of a gene signature for citrate-spermine secretion derived from ST with metabolic measurements from MSI.
conclusionMIIT is a highly accurate, customizable, open-source framework for integrating spatial omics technologies performed on different serial sections.
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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.