Multi-modal image analysis for large-scale cancer tissue studies within IMMUcan
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.
Authors
- Nils Eling (ORCID: https://orcid.org/0000-0002-4711-1176)
- Michelle M. Daniel (ORCID: https://orcid.org/0000-0001-8961-7119)
- Bernd Bodenmiller (ORCID: https://orcid.org/0000-0002-6325-7861)
- Sylvie Rusakiewicz (ORCID: https://orcid.org/0000-0001-5939-5690)
- George Coukos (ORCID: https://orcid.org/0000-0001-8813-7367)
- Sébastien Déglise (ORCID: https://orcid.org/0000-0001-8244-952X)
- Ewa Szczurek (ORCID: https://orcid.org/0000-0002-1320-6695)
- Henoch S. Hong (ORCID: https://orcid.org/0000-0002-3367-1738)
- Nikesh Parsotam
- Marcin Możejko (ORCID: https://orcid.org/0000-0002-5631-0046)
- Alexander Loboda (ORCID: https://orcid.org/0000-0002-0285-5841)
- Nicolas Guex (ORCID: https://orcid.org/0000-0001-6023-0519)
- Julien Dorier (ORCID: https://orcid.org/0000-0002-6717-2451)
- Abdelkader Benyagoub
- Daniel Schulz (ORCID: https://orcid.org/0000-0002-0913-1678)
- Jonas Windhager (ORCID: https://orcid.org/0000-0002-2111-5291)
- Marie Morfouace (ORCID: https://orcid.org/0000-0002-3958-3755)
- Robin Liechti (ORCID: https://orcid.org/0000-0001-8351-4776)
- Stephanie Tissot
- Lucie Despland
- Bruno Palau Fernandez (ORCID: https://orcid.org/0009-0005-7433-7516)
- P Devanand
- Daaf Sandkuijl
- Dawid Uchal
Institutions
- SIB Swiss Institute of Bioinformatics (CH)
- Merck KGaA, Darmstadt (Germany) (DE)
- Institut Gustave Roussy (FR)
- Centre Hospitalier Universitaire Vaudois (CH)
- Helmholtz Zentrum München (DE)
- ETH Zurich (CH)
- Standard Bio (Norway) (NO)
- Ludwig Cancer Research (CH)
- Life Science Zurich (CH)
- University of Warsaw (PL)
- University of Lausanne (CH)
Publication Details
- Journal
- Cell Reports Methods
- Published
- 2025-09-01
- DOI
- https://doi.org/10.1016/j.crmeth.2025.101170
- Citations
- 1
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- European Federation of Pharmaceutical Industries and Associations
- Alliance Healthcare Foundation
- European Commission