MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
<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 de...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2023
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| Online Access: | https://hdl.handle.net/1721.1/147096 |
| _version_ | 1826193904397975552 |
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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 |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology 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 | MIT |
| description | <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> |
| first_indexed | 2024-09-23T09:47:09Z |
| format | Article |
| id | mit-1721.1/147096 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:47:09Z |
| publishDate | 2023 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1470962023-01-14T03:39:37Z 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 Massachusetts Institute of Technology. Department of Biology <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> 2023-01-13T15:00:40Z 2023-01-13T15:00:40Z 2022 2023-01-13T14:37:17Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/147096 Schapiro, 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). en 10.1038/S41592-021-01308-Y Nature Methods Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | 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 |
| url | https://hdl.handle.net/1721.1/147096 |
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