IMCWorkshop2026

This is the official data repository for the IMC workshop 2026, hosted by the Bodenmiller lab at the University of Zurich / ETH Zurich. This imaging mass cytometry (IMC) dataset serves as an example to demonstrate raw data processing and downstream analysis tools. The data was generated as part of the Integrated iMMUnoprofiling of large adaptive CANcer patient cohorts (IMMUcan) project (immucan.eu) using the Hyperion imaging system (www.fluidigm.com/products-services/instruments/hyperion). To get an overview on the technology and available analysis strategies, please visit bodenmillergroup.github.io/IMCWorkflow. The individual data files are described below: cell_mode: folder raw with standard 1 $\mu$m resolution raw data files of 4 patient samples (Patient1.zip, Patient2.zip, Patient3.zip, Patient4.zip). Each .zip archive contains a folder in which one .mcd file (IMC raw data) and multiple .txt files (one per acquisition) can be found. folder masks contains segmentation masks extracted with steinbock deepcell. folder masks_cellpose_sam contains segmentation masks extracted with novel cellposeSAM model (https://github.com/MouseLand/cellpose). folder masks_instanseg contains segmentation masks extracted with novel InstanSeg model (https://github.com/instanseg/instanseg). folder img_dimr contains images corrected with IMC-Denoise (https://github.com/PENGLU-WashU/IMC_Denoise). panel_clean.csv: This file contains metadata for each antibody/channel used in the experiment. The full column indicates which channel should be analysed. The ilastik, cellpose, deepcell columns indicate the channels used for cell segmentation. preview_mode: folder img with a low resolution IMC image (.tiff), acquired by skipping pixels in x,y during acquisition, but whole slide. folder masks with a tissue mask from the preview image. compensation: This folder contains 2 spillover compensation raw data. This data is used for channel spillover correction. For more information, please refer to the original publication: Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry 1. A folder txt with .txt files for spillover compensation on older systems. 2. an .mcd file in folder raw for newer systems (XTi). sample_metadata.csv: This file links each patient to their cancer type (SCCHN - head and neck cancer; BCC - breast cancer; NSCLC - lung cancer; CRC - colorectal cancer).