Single-cell information extracted from IMC example 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 repository contains additional information related to IMC example data available at zenodo.org/record/5949116. The following files are available and are part of the IMC Data Analysis workflow

• gated_cells.zip: contains SpatialExperiment objects storing cells that were manually gated based on their expression values to derive ground truth cell phenotype labels.
• spe.rds: SpatialExperiment object containing the single-cell information (mean intensity per cell and per channel; cellular metadata; channel metadata) of the processed data.
• images.rds: CytoImageList object containing the spillover-corrected images.
• masks.rds: CytoImageList object containing the segmentation masks.