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

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.; Coussens, L. M.; Santagata, S.; Sorger, P. K.

doi:10.1101/2021.03.15.435473

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bioRxiv · 10.1101/2021.03.15.435473

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

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Abstract

Highly 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.

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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., Coussens, L. M., Santagata, S., Sorger, P. K.. 2021-03-16. MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging. https://doi.org/10.1101/2021.03.15.435473

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