Imaging mass cytometry based immune profiling of human Peyer´s patches in patients of Crohn's disease

This dataset contains all relevant data used in the publication Imaging mass cytometry based immune profiling of human Peyer´s patches in patients of Crohn’s disease published in the European Journal of Immunology. The data was spillover corrected before background removal and processed using the imcRtools and cytomapper R-packages as published in Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc (2023). The dataset contains: images.rds: The background corrected IMC images AnnotatedRegions.7z: The manually annotated tissue regions as tiff-images. Individual values correspond to the respective tissue region. spePaper.rds: The single cell data object (including respective metadata) masks.rds: The single cell masks.