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MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
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, MC...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Nature Publishing Group US
2021
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8916956/ https://www.ncbi.nlm.nih.gov/pubmed/34824477 http://dx.doi.org/10.1038/s41592-021-01308-y |
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| author | Schapiro, Denis Sokolov, Artem Yapp, Clarence Chen, Yu-An Muhlich, Jeremy L. Hess, Joshua Creason, Allison L. Nirmal, Ajit J. Baker, Gregory J. Nariya, Maulik K. Lin, Jia-Ren Maliga, Zoltan Jacobson, Connor A. Hodgman, Matthew W. Ruokonen, Juha Farhi, Samouil L. Abbondanza, Domenic McKinley, Eliot T. Persson, Daniel Betts, Courtney Sivagnanam, Shamilene Regev, Aviv Goecks, Jeremy Coffey, Robert J. Coussens, Lisa M. Santagata, Sandro Sorger, Peter K. |
| author_facet | Schapiro, Denis Sokolov, Artem Yapp, Clarence Chen, Yu-An Muhlich, Jeremy L. Hess, Joshua Creason, Allison L. Nirmal, Ajit J. Baker, Gregory J. Nariya, Maulik K. Lin, Jia-Ren Maliga, Zoltan Jacobson, Connor A. Hodgman, Matthew W. Ruokonen, Juha Farhi, Samouil L. Abbondanza, Domenic McKinley, Eliot T. Persson, Daniel Betts, Courtney Sivagnanam, Shamilene Regev, Aviv Goecks, Jeremy Coffey, Robert J. Coussens, Lisa M. Santagata, Sandro Sorger, Peter K. |
| author_sort | Schapiro, Denis |
| collection | PubMed |
| description | 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. |
| format | Online Article Text |
| id | pubmed-8916956 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2021 |
| publisher | Nature Publishing Group US |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-89169562022-03-15 MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging Schapiro, Denis Sokolov, Artem Yapp, Clarence Chen, Yu-An Muhlich, Jeremy L. Hess, Joshua Creason, Allison L. Nirmal, Ajit J. Baker, Gregory J. Nariya, Maulik K. Lin, Jia-Ren Maliga, Zoltan Jacobson, Connor A. Hodgman, Matthew W. Ruokonen, Juha Farhi, Samouil L. Abbondanza, Domenic McKinley, Eliot T. Persson, Daniel Betts, Courtney Sivagnanam, Shamilene Regev, Aviv Goecks, Jeremy Coffey, Robert J. Coussens, Lisa M. Santagata, Sandro Sorger, Peter K. Nat Methods Brief Communication 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. Nature Publishing Group US 2021-11-25 2022 /pmc/articles/PMC8916956/ /pubmed/34824477 http://dx.doi.org/10.1038/s41592-021-01308-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
| spellingShingle | Brief Communication Schapiro, Denis Sokolov, Artem Yapp, Clarence Chen, Yu-An Muhlich, Jeremy L. Hess, Joshua Creason, Allison L. Nirmal, Ajit J. Baker, Gregory J. Nariya, Maulik K. Lin, Jia-Ren Maliga, Zoltan Jacobson, Connor A. Hodgman, Matthew W. Ruokonen, Juha Farhi, Samouil L. Abbondanza, Domenic McKinley, Eliot T. Persson, Daniel Betts, Courtney Sivagnanam, Shamilene Regev, Aviv Goecks, Jeremy Coffey, Robert J. Coussens, Lisa M. Santagata, Sandro Sorger, Peter K. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| title | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| title_full | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| title_fullStr | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| title_full_unstemmed | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| title_short | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| title_sort | mcmicro: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| topic | Brief Communication |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8916956/ https://www.ncbi.nlm.nih.gov/pubmed/34824477 http://dx.doi.org/10.1038/s41592-021-01308-y |
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