Multi-modal image analysis for large scale cancer tissue studies within IMMUcan

MotivationMultiplexed imaging is increasingly used to study tissue architecture in health and disease. To investigate the cancer tumor microenvironment, typically either tissue micro-arrays or small patient cohorts are used to collect and process data. However, studies performed over the course of years, collecting data from thousands of samples are rare and require specialized workflows to ensure sample throughput and reproducibility for data production and processing. Here, we present two such workflows for multiplexed immunofluorescence and imaging mass cytometry of cancer tissues which are applied to a total of roughly 10000 samples from 2500 patients over six years. SummaryIn cancer research, multiplexed imaging allows detailed characterization of the tumor microenvironment (TME) and its link to patient prognosis. The IMMUcan consortium collects multi-modal imaging data from thousands of cancer patients to perform broad molecular and cellular spatial profiling across five cancer indications. Here, we describe two workflows for multiplexed immunofluorescence (mIF) and imaging mass cytometry (IMC) developed within IMMUcan to enable analysis of thousands of cancer tissues. IFQuant supports web-based, user-friendly, and reproducible analysis of mIF data. High sample throughput for IMC is achieved by optimizing experimental protocols and developing a robotic arm for automated slide loading. We provide a resource of 350000 manually labelled cells across 180 cancer samples to accurately annotate cell phenotypes in IMC. All major cell phenotypes and tissue structures correlate well between mIF and IMC. These pipelines form the basis for multiplexed image analysis within IMMUcan and provide computational tools for the larger community.