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.
Competing Interest Statement
PKS is a member of the SAB or BOD member of Applied Biomath, RareCyte Inc., and Glencoe Software, which distributes a commercial version of the OMERO database; PKS is also a member of the NanoString SAB. In the last five years the Sorger lab has received research funding from Novartis and Merck. Sorger declares that none of these relationships have influenced the content of this manuscript. SS is a consultant for RareCyte Inc. A. R. is a cofounder and equity holder of Celsius Therapeutics, an equity holder in Immunitas and, until 31 July 2020, was an SAB member of Thermo Fisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov. Since August 1, 2020, A. R. has been an employee of Genentech. The other authors declare no outside interests.
