MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu‐An Chen, Jeremy L. Muhlich, Joshua M. Hess, Allison Creason, Ajit J. Nirmal, Gregory J. Baker, Maulik K. Nariya, Jia‐Ren Lin, Zoltan Maliga, Connor A. Jacobson, Matthew Hodgman, Juha Ruokonen, Samouil L. Farhi, Domenic Abbondanza, Eliot T. McKinley, Daniel Persson, Courtney B. Betts, Shamilene Sivagnanam, Aviv Regev, Jeremy Goecks, Robert J. Coffey, Lisa M. Coussens, Sandro Santagata, Peter K. Sorger
Abstract
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.