MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging
Nature Methods, 2021
Schapiro, D., Sokolov, A., Yapp, C., Muhlich, J. L., Hess, J., Lin, J.R., Chen, Y.A., Nariya, M.K., Baker, G.J., Ruokonen, J., Maliga Z., Jacobson C.A., Farhi S.L., Abbondanza, D., McKinley, E.T., Betts, C. Regev A., Coffey R.J., Lisa M., Coussens, L.M., Santagata, S., and Sorger P.K.
Abstract
Highly multiplexed tissue imaging makes molecular analysis of singlecells possible in a preserved spatial context. However,reproducible analysis of the underlying data posesa substantial computational challenge. Here we describe a modular and open-source computational pipeline (MCMICRO) for performing the sequential steps needed to transform large, multi-channelwhole slide images into single-cell data. We demonstrate use of MCMICRO on images of different tissues and tumors acquired using multiple imagingplatforms, thereby providing a solid foundation for the continueddevelopment of tissue imaging software.