Example imaging mass cytometry raw data

If you are working with these files, please cite them as follows:

Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc (2023). https://doi.org/10.1038/s41596-023-00881-0

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:

• Patient1.zip, Patient2.zip, Patient3.zip, Patient4.zip: raw data files of 4 patient samples. Each .zip archive contains a folder in which one .mcd file (IMC raw data) and multiple .txt files (one per acquisition) can be found.
• compensation.zip: This .zip archive holds a folder which contains one .mcd file and multiple .txt files. Multiple spots of a "spillover slide" were acquired and each .txt file is named based on the spotted metal. 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
• panel.csv: This file contains metadata for each antibody/channel used in the experiment. The full column indicates which channel should be analysed. The ilastik column specifies which channels were used for ilastik pixel classification and the deepcell column indicates the channels used for deepcell segmentation.
• 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).