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

dc.contributor.authorSchapiro, Denis
dc.contributor.authorSokolov, Artem
dc.contributor.authorYapp, Clarence
dc.contributor.authorChen, Yu-An
dc.contributor.authorMuhlich, Jeremy L
dc.contributor.authorHess, Joshua
dc.contributor.authorCreason, Allison L
dc.contributor.authorNirmal, Ajit J
dc.contributor.authorBaker, Gregory J
dc.contributor.authorNariya, Maulik K
dc.contributor.authorLin, Jia-Ren
dc.contributor.authorMaliga, Zoltan
dc.contributor.authorJacobson, Connor A
dc.contributor.authorHodgman, Matthew W
dc.contributor.authorRuokonen, Juha
dc.contributor.authorFarhi, Samouil L
dc.contributor.authorAbbondanza, Domenic
dc.contributor.authorMcKinley, Eliot T
dc.contributor.authorPersson, Daniel
dc.contributor.authorBetts, Courtney
dc.contributor.authorSivagnanam, Shamilene
dc.contributor.authorRegev, Aviv
dc.contributor.authorGoecks, Jeremy
dc.contributor.authorCoffey, Robert J
dc.contributor.authorCoussens, Lisa M
dc.contributor.authorSantagata, Sandro
dc.contributor.authorSorger, Peter K
dc.date.accessioned2023-01-13T15:00:40Z
dc.date.available2023-01-13T15:00:40Z
dc.date.issued2022
dc.identifier.urihttps://hdl.handle.net/1721.1/147096
dc.description.abstract<jats:title>Abstract</jats:title><jats:p>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.</jats:p>en_US
dc.language.isoen
dc.publisherSpringer Science and Business Media LLCen_US
dc.relation.isversionof10.1038/S41592-021-01308-Yen_US
dc.rightsCreative Commons Attribution 4.0 International licenseen_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.sourceNatureen_US
dc.titleMCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imagingen_US
dc.typeArticleen_US
dc.identifier.citationSchapiro, Denis, Sokolov, Artem, Yapp, Clarence, Chen, Yu-An, Muhlich, Jeremy L et al. 2022. "MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging." Nature Methods, 19 (3).
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biologyen_US
dc.relation.journalNature Methodsen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dc.date.updated2023-01-13T14:37:17Z
dspace.orderedauthorsSchapiro, D; Sokolov, A; Yapp, C; Chen, Y-A; Muhlich, JL; Hess, J; Creason, AL; Nirmal, AJ; Baker, GJ; Nariya, MK; Lin, J-R; Maliga, Z; Jacobson, CA; Hodgman, MW; Ruokonen, J; Farhi, SL; Abbondanza, D; McKinley, ET; Persson, D; Betts, C; Sivagnanam, S; Regev, A; Goecks, J; Coffey, RJ; Coussens, LM; Santagata, S; Sorger, PKen_US
dspace.date.submission2023-01-13T14:37:21Z
mit.journal.volume19en_US
mit.journal.issue3en_US
mit.licensePUBLISHER_CC
mit.metadata.statusAuthority Work and Publication Information Neededen_US


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