MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
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ABSTRACT:
SUBMITTER: Schapiro D
PROVIDER: S-EPMC8916956 | biostudies-literature | 2022 Mar
REPOSITORIES: biostudies-literature
Publications
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro Denis D Sokolov Artem A Yapp Clarence C Chen Yu-An YA Muhlich Jeremy L JL Hess Joshua J Creason Allison L AL Nirmal Ajit J AJ Baker Gregory J GJ Nariya Maulik K MK Lin Jia-Ren JR Maliga Zoltan Z Jacobson Connor A CA Hodgman Matthew W MW Ruokonen Juha J Farhi Samouil L SL Abbondanza Domenic D McKinley Eliot T ET Persson Daniel D Betts Courtney C Sivagnanam Shamilene S Regev Aviv A Goecks Jeremy J Coffey Robert J RJ Coussens Lisa M LM Santagata Sandro S Sorger Peter K PK
Nature methods 20211125 3
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 pl ...[more]
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