Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer

All data supporting the publication: "Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer."
1. Fully_Processed_OME.TIFF: This folder contains the OME.TIFF files with all markers after compensation and hot pixel removal for visualization of the data. These can be opened with QuPath and other software. 
2. PDAC_IMC_Seurat_FINAL.rds: Seurat object of all cells included in the analysis with cell type and neighborhood annotations, and unintegrated and rPCA-integrated UMAP reductions. 
3. Raw_Data_TIFF_Files: All raw individual TIFF files from the image acquisition
4. ROI_Selection: Brightfield and IHC images of individual samples showing where the ROIs for each sample are collected 
5. Segmentation_Files: All relevant segmentation files from Mesmer for nuclear and whole cell segmentation. 
6. H&E Images for each case scanned at 40x