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

Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. Epub 2021 Nov 25.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Diagnostic Imaging
  • Humans
  • Image Processing, Computer-Assisted* / methods
  • Neoplasms* / diagnostic imaging
  • Neoplasms* / pathology
  • Software