MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

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. MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data.