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MCMICRO: A Scalable, Modular Image-processing Pipeline For Multiplexed Tissue Imaging

Denis Schapiro, Artem Sokolov, Clarence Yapp, Jeremy L. Muhlich, Joshua Hess, Jia-Ren Lin, Yu-An Chen, Maulik K. Nariya, Gregory J. Baker, Juha Ruokonen, Zoltan Maliga, Connor A. Jacobson, Samouil L. Farhi, Domenic Abbondanza, Eliot T. McKinley, Courtney Betts, Aviv Regev, Robert J. Coffey, Lisa M. Coussens, Sandro Santagata, Peter K. Sorger

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ABSTRACTHighly multiplexed tissue imaging makes molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of the underlying data poses a substantial computational challenge. Here we describe a modular and open-source computational pipeline (MCMICRO) for performing the sequential steps needed to transform large, multi-channel whole slide images into single-cell data. We demonstrate use of MCMICRO on images of different tissues and tumors acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.