End-to-end microscopy imaging with MCMICRO and MCMICRO for HTAN

Our October webinar features the MCMICRO software tool on the Cancer Genomics Cloud, originally developed by collaborators in the Human Tumor Atlas Network (HTAN) consortium. MCMICRO is designed for detailed analysis of cellular structures through highly multiplexed tissue imaging – that is, whole-slide tissue imaging of samples with multiple channels of protein antibody staining. Analysis of these images makes the resolution of spatial sequencing data possible, underpinning techniques such as single-cell spatial transcriptomics, but presents several challenges to researchers. MCMICRO handles much of the processing in a single pipeline.  

Presenters Rowan Beck and Boris Majić will discuss the tool's development, including its availability in both NextFlow and Common Workflow Language formats on CGC and ongoing efforts for Galaxy integration. The discussion will include practical insights into MCMICRO's functionality in processing whole-slide images into single-cell data, using various tissue and tumor imaging platforms. Participants will learn about the software's specifications, operation, and application in research settings. 

For additional information, refer to the full paper: MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging 

About the speakers

Boris Majić is a Bioinformatics Analyst at Velsera. Mr. Majić holds a Master’s degree in Signal Processing and a Bachelor’s degree in Electrical Engineering.

Rowan Beck is a Community Engagement Manager at Velsera. Dr. Beck holds a PhD in Genetics and Molecular Biology from the University of North Carolina at Chapel Hill.

Mr. Boris Majic

Dr. Rowan Beck