Abstract

Multiplex tissue images are large, multi-channel images that contain intensity data for numerous biomarkers. The methods for generating multiplex tissue images are diverse, and each method can require specialized knowledge for downstream processing and analysis. The MCMICRO pipeline was developed to process multiplex images into single-cell data, and to have the range of tools to accomodate for different imaging methods. The tools used in the MCMICRO pipeline, in addition to tools for single-cell analysis, spatial analysis, and interactive visualization are available in Galaxy to facilitate comprehensive and accessible analyses of multiplex tissue images. The MCMICRO tools available in Galaxy are capable of processing Whole Slide Images (WSI) and Tissue Microarrays (TMA). WSIs are images in which a tissue section from a single sample occupies the entire microscope slide; whereas, TMAs multiplex smaller cores from multiple samples onto a single slide. This tutorial will demonstrate how to use the Galaxy multiplex imaging tools to process and analyze publicly available TMA test data provided by MCMICRO (Figure 1.).

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What tools are available for pre-processing multiplex tissue images in Galaxy?
• What tools are available for downstream analysis of multiplex tissue images in Galaxy?
• How do I pre-process and analyze Tissue Microarray data?
• How can I visualize multiplex tissue images and associated data?
• How can I assign phenotypes to cells in an MTI dataset?

Learning Objectives

• Understand the tools available in Galaxy for multiplex tissue imaging analysis
• Analyze and visualize publicly available TMA data using Galaxy