"Paneth cells modulate intestinal lymphatic vessels and lipid metabolism in metabolic dysfunction-associated steatotic liver disease" IMC dataset

This upload contains the raw and processed IMC dataset from the publication. The files include: Raw IMC dataset in the archive "imc_raw.zip" Segmentation masks for each slide obtained used steinpose napari plugin in "masks.zip", cellpose v2 parameters included Processed with steinbock package raw R dataset from 2 rounds of acquisition in "spe_dr_round1.rds" and "spe_dr_round2.rds" Manual cell annotation table in "annotation_manual.zip", parameters included Fully analyzed merged R dataset in "spe_final.rds" Script for analysis and figures in "analysis_script.R" Differential abundance results for cell types and regions in "differential_abundance_celltypes.xlsx" and "differential_abundance_region.xlsx" Endothelial cell clustering and classification results in ec_stats.csv