ArticleCell reports methods2025
Multi-modal image analysis for large-scale cancer tissue studies within IMMUcan.
Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Multimodal Imaging of the Cellular and Extracellular Microenvironment on the Same Formalin-Fixed Paraffin-Embedded Tissue Section.bioRxiv : the preprint server for biology · 2026Article
- Molecular and Immune Landscape of Recurrent and/or Distant Metastatic Squamous Cell Carcinoma of the Head and Neck: An EORTC/IMMUCAN Project.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.BMC bioinformatics · 2026Article
- Predicting Response to Immune Checkpoint Inhibitors in Melanoma: Emerging Approaches in Digital Pathology, Spatial Profiling and Machine Learning.International journal of molecular sciences · 2026Review
- OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.Research square · 2026Article
- Topography-aware optimal transport for alignment of spatial omics data.Cell reports methods · 2026Article
- Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment.Cancer immunology research · 2026Article
- Article
- Spatially-smoothed quantification improves cell typing in imaging mass cytometry datasets.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
24 authors.
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Abstract
In cancer research, multiplexed imaging allows detailed characterization of the tumor microenvironment (TME) and its link to patient prognosis. The integrated immunoprofiling of large adaptive cancer patient cohorts (IMMUcan) consortium collects multi-modal imaging data from thousands of patients with cancer to perform broad molecular and cellular spatial profiling. Here, we describe and compare two workflows for multiplexed immunofluorescence (mIF) and imaging mass cytometry (IMC) developed within IMMUcan to enable the generation of standardized data for cancer tissue analysis. The IFQuant software supports web-based, user-friendly, and reproducible analysis of mIF data. High sample throughput for IMC is achieved by optimizing experimental protocols, developing a robotic arm for automated slide loading, and classification-based cell typing. Using our manually labeled single-cell data, we show that tree-based methods outperform other cell-phenotyping tools. These pipelines form the basis for multiplexed image analysis within IMMUcan, and we summarize our learnings from 5 years of development and optimization.
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