This is a companion release for the manuscript titled "Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section" (biorxiv doi: 10.1101/2022.09.28.509927) The dataset index and scripts for processing and analysis are deposited in the latest release. The same files can also be found by following the link under "Related identifiers". This work was supported by NCI grants U54-CA225088 and U2C-CA233262 (PKS, SS), an NCI SBIR small business grant to RareCyte and PKS (R41-CA224503), and commercial investment from RareCyte; data processing software was developed with support from a Team Science Grant from the Gray Foundation and Ludwig Cancer Research (PKS, SS). SS is supported by the BWH President’s Scholars Award.