@article{a61fab7143d14dea91a487655ad462bf,
title = "MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging",
abstract = "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.",
author = "Denis Schapiro and Artem Sokolov and Clarence Yapp and Chen, {Yu An} and Muhlich, {Jeremy L.} and Joshua Hess and Creason, {Allison L.} and Nirmal, {Ajit J.} and Baker, {Gregory J.} and Nariya, {Maulik K.} and Lin, {Jia Ren} and Zoltan Maliga and Jacobson, {Connor A.} and Hodgman, {Matthew W.} and Juha Ruokonen and Farhi, {Samouil L.} and Domenic Abbondanza and McKinley, {Eliot T.} and Daniel Persson and Courtney Betts and Shamilene Sivagnanam and Aviv Regev and Jeremy Goecks and Coffey, {Robert J.} and Coussens, {Lisa M.} and Sandro Santagata and Sorger, {Peter K.}",
note = "Funding Information: We thank all early adopters of MCMICRO, particularly R. Pelletier, E. Novikov, J. Davis, H. Udhani, T. Vallius, C. Ritch and N. Girnius. This work was funded by National Institutes of Health (NIH) grants U54-CA225088 and U2C-CA233262 to P.K.S. and S. Santagata and by the Ludwig Cancer Center at Harvard. D.S. was funded by an Early Postdoc Mobility fellowship (no. P2ZHP3_181475) from the Swiss National Science Foundation and is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRQ-03-20). Z.M. is supported by NCI grant R50-CA252138. We thank the Dana-Farber/Harvard Cancer Center in Boston, MA, for the use of the Specialized Histopathology Core, which provided TMA construction and sectioning services. The Dana-Farber/Harvard Cancer Center is supported in part by NCI Cancer Center Support Grant P30 CA06516. Tissue samples were provided by the NCI Cooperative Human Tissue Network (CHTN). L.M.C. acknowledges funding from the National Institutes of Health (1U01 CA224012, U2C-CA233280, R01-CA223150, R01-CA226909, R21-HD099367), the Knight Cancer Institute and the Brenden-Colson Center for Pancreatic Care at OHSU. Development of analytical methods used for image analysis at OHSU were developed and carried out with major support from the NIH, National Cancer Institute Human Tumor Atlas Network (HTAN) Research Center (U2C-CA233280) and the Prospect Creek Foundation to the OHSU SMMART (Serial Measurement of Molecular and Architectural Responses to Therapy) Program. Funding Information: P.K.S. 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; P.K.S. is also a member of the NanoString SAB. In the last 5years, the Sorger laboratory has received research funding from Novartis and Merck. Sorger declares that none of these relationships have influenced the content of this manuscript. S. Santagata is a consultant for RareCyte Inc. A.R. is a cofounder and equity holder of Celsius Therapeutics, an equity holder in Immunitas and, until 31July 2020, was an SAB member of Thermo Fisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov. Since 1 August 2020, A.R. has been an employee of Genentech. L.M.C. is a paid consultant for Cell Signaling Technologies, AbbVie Inc. and Shasqi Inc.; received reagent and/or research support from Plexxikon Inc., Pharmacyclics, Inc., Acerta Pharma, LLC, Deciphera Pharmaceuticals, LLC, Genentech, Inc., Roche Glycart AG, Syndax Pharmaceuticals Inc., Innate Pharma, NanoString Technologies and Cell Signaling Technologies; is a member of the Scientific Advisory Boards of Syndax Pharmaceuticals, Carisma Therapeutics, Zymeworks, Inc., Verseau Therapeutics, Cytomix Therapeutics, Inc. and Kineta Inc. and is a member of the Lustgarten Therapeutics Advisory working group. D.S. is a consultant for Roche Glycart AG. The other authors declare no outside interests. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2022",
month = mar,
doi = "10.1038/s41592-021-01308-y",
language = "English (US)",
volume = "19",
pages = "311--315",
journal = "PLoS Medicine",
issn = "1549-1277",
publisher = "Nature Publishing Group",
number = "3",
}