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...
Gespeichert in:
| Veröffentlicht in: | Nature methods 2022-03, Vol.19 (3), p.311-315 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 315 |
|---|---|
| container_issue | 3 |
| container_start_page | 311 |
| container_title | Nature methods |
| container_volume | 19 |
| creator | 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. |
| 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.
MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data. |
| doi_str_mv | 10.1038/s41592-021-01308-y |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8916956</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2638176749</sourcerecordid><originalsourceid>FETCH-LOGICAL-c474t-c1c70bf169bc9416d4babd1c57d1d466af3b7b7e9513fd057aa0c7967601aa13</originalsourceid><addsrcrecordid>eNp9kUtr3DAUhUVJaR7tH-giGLLJok50LVmyuwiEoXlAQqCkayHL11MF2XIlO3T-fZWZPLvISoL7nXMfh5CvQI-Asuo4cijrIqcF5BQYrfLVB7IDJa9yCbTcevrTGrbJbox3lDLGi_IT2Wa8KjiXcof8ul5cXy5-3nzPdBaNdrpx-C3rfTs7HTLb6yXmY_AGY7TDMhvtiM4OmHU-ZP3sJjs6_IttNtkYZ1wLEveZfOy0i_jl8d0jt2c_bhcX-dXN-eXi9Co3XPIpN2AkbToQdWNqDqLljW5aMKVsoeVC6I41spFYl8C6lpZSa2pkLaSgoDWwPXKysR3npsfW4DAF7dQY0hhhpby26m1lsL_V0t-rqk49S5EMDh8Ngv8zY5xUb6NB5_SAfo6qEJSn04KUCT34D73zcxjSdoliFUgheZ2oYkOZ4GMM2D0PA1Q9hKY2oakUmlqHplZJtP96jWfJU0oJYBsgptKwxPDS-x3bf5Ino88</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2638176749</pqid></control><display><type>article</type><title>MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging</title><source>MEDLINE</source><source>Nature Journals Online</source><source>SpringerLink Journals - AutoHoldings</source><creator>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.</creator><creatorcontrib>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.</creatorcontrib><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.
MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data.</description><identifier>ISSN: 1548-7091</identifier><identifier>ISSN: 1548-7105</identifier><identifier>EISSN: 1548-7105</identifier><identifier>DOI: 10.1038/s41592-021-01308-y</identifier><identifier>PMID: 34824477</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/114/1564 ; 631/114/794 ; 631/553 ; Bioinformatics ; Biological Microscopy ; Biological Techniques ; Biomedical and Life Sciences ; Biomedical Engineering/Biotechnology ; Brief Communication ; Computer applications ; Diagnostic Imaging ; Humans ; Image acquisition ; Image processing ; Image Processing, Computer-Assisted - methods ; Life Sciences ; Multiplexing ; Neoplasms - diagnostic imaging ; Neoplasms - pathology ; Proteomics ; Software ; Spatial analysis ; Tissues ; Tumors</subject><ispartof>Nature methods, 2022-03, Vol.19 (3), p.311-315</ispartof><rights>The Author(s) 2021</rights><rights>2021. The Author(s).</rights><rights>The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-c1c70bf169bc9416d4babd1c57d1d466af3b7b7e9513fd057aa0c7967601aa13</citedby><cites>FETCH-LOGICAL-c474t-c1c70bf169bc9416d4babd1c57d1d466af3b7b7e9513fd057aa0c7967601aa13</cites><orcidid>0000-0003-2389-1865 ; 0000-0003-1359-4568 ; 0000-0002-3364-1838 ; 0000-0003-4702-7705 ; 0000-0003-3293-3158 ; 0000-0002-4583-5226 ; 0000-0002-2180-3844 ; 0000-0001-5724-1276 ; 0000-0002-8056-0504 ; 0000-0003-1144-5710 ; 0000-0002-0811-637X ; 0000-0002-5196-3961 ; 0000-0002-0299-3451 ; 0000-0003-3776-1092</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41592-021-01308-y$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41592-021-01308-y$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,777,781,882,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34824477$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schapiro, Denis</creatorcontrib><creatorcontrib>Sokolov, Artem</creatorcontrib><creatorcontrib>Yapp, Clarence</creatorcontrib><creatorcontrib>Chen, Yu-An</creatorcontrib><creatorcontrib>Muhlich, Jeremy L.</creatorcontrib><creatorcontrib>Hess, Joshua</creatorcontrib><creatorcontrib>Creason, Allison L.</creatorcontrib><creatorcontrib>Nirmal, Ajit J.</creatorcontrib><creatorcontrib>Baker, Gregory J.</creatorcontrib><creatorcontrib>Nariya, Maulik K.</creatorcontrib><creatorcontrib>Lin, Jia-Ren</creatorcontrib><creatorcontrib>Maliga, Zoltan</creatorcontrib><creatorcontrib>Jacobson, Connor A.</creatorcontrib><creatorcontrib>Hodgman, Matthew W.</creatorcontrib><creatorcontrib>Ruokonen, Juha</creatorcontrib><creatorcontrib>Farhi, Samouil L.</creatorcontrib><creatorcontrib>Abbondanza, Domenic</creatorcontrib><creatorcontrib>McKinley, Eliot T.</creatorcontrib><creatorcontrib>Persson, Daniel</creatorcontrib><creatorcontrib>Betts, Courtney</creatorcontrib><creatorcontrib>Sivagnanam, Shamilene</creatorcontrib><creatorcontrib>Regev, Aviv</creatorcontrib><creatorcontrib>Goecks, Jeremy</creatorcontrib><creatorcontrib>Coffey, Robert J.</creatorcontrib><creatorcontrib>Coussens, Lisa M.</creatorcontrib><creatorcontrib>Santagata, Sandro</creatorcontrib><creatorcontrib>Sorger, Peter K.</creatorcontrib><title>MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging</title><title>Nature methods</title><addtitle>Nat Methods</addtitle><addtitle>Nat Methods</addtitle><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.
MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data.</description><subject>631/114/1564</subject><subject>631/114/794</subject><subject>631/553</subject><subject>Bioinformatics</subject><subject>Biological Microscopy</subject><subject>Biological Techniques</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedical Engineering/Biotechnology</subject><subject>Brief Communication</subject><subject>Computer applications</subject><subject>Diagnostic Imaging</subject><subject>Humans</subject><subject>Image acquisition</subject><subject>Image processing</subject><subject>Image Processing, Computer-Assisted - methods</subject><subject>Life Sciences</subject><subject>Multiplexing</subject><subject>Neoplasms - diagnostic imaging</subject><subject>Neoplasms - pathology</subject><subject>Proteomics</subject><subject>Software</subject><subject>Spatial analysis</subject><subject>Tissues</subject><subject>Tumors</subject><issn>1548-7091</issn><issn>1548-7105</issn><issn>1548-7105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kUtr3DAUhUVJaR7tH-giGLLJok50LVmyuwiEoXlAQqCkayHL11MF2XIlO3T-fZWZPLvISoL7nXMfh5CvQI-Asuo4cijrIqcF5BQYrfLVB7IDJa9yCbTcevrTGrbJbox3lDLGi_IT2Wa8KjiXcof8ul5cXy5-3nzPdBaNdrpx-C3rfTs7HTLb6yXmY_AGY7TDMhvtiM4OmHU-ZP3sJjs6_IttNtkYZ1wLEveZfOy0i_jl8d0jt2c_bhcX-dXN-eXi9Co3XPIpN2AkbToQdWNqDqLljW5aMKVsoeVC6I41spFYl8C6lpZSa2pkLaSgoDWwPXKysR3npsfW4DAF7dQY0hhhpby26m1lsL_V0t-rqk49S5EMDh8Ngv8zY5xUb6NB5_SAfo6qEJSn04KUCT34D73zcxjSdoliFUgheZ2oYkOZ4GMM2D0PA1Q9hKY2oakUmlqHplZJtP96jWfJU0oJYBsgptKwxPDS-x3bf5Ino88</recordid><startdate>20220301</startdate><enddate>20220301</enddate><creator>Schapiro, Denis</creator><creator>Sokolov, Artem</creator><creator>Yapp, Clarence</creator><creator>Chen, Yu-An</creator><creator>Muhlich, Jeremy L.</creator><creator>Hess, Joshua</creator><creator>Creason, Allison L.</creator><creator>Nirmal, Ajit J.</creator><creator>Baker, Gregory J.</creator><creator>Nariya, Maulik K.</creator><creator>Lin, Jia-Ren</creator><creator>Maliga, Zoltan</creator><creator>Jacobson, Connor A.</creator><creator>Hodgman, Matthew W.</creator><creator>Ruokonen, Juha</creator><creator>Farhi, Samouil L.</creator><creator>Abbondanza, Domenic</creator><creator>McKinley, Eliot T.</creator><creator>Persson, Daniel</creator><creator>Betts, Courtney</creator><creator>Sivagnanam, Shamilene</creator><creator>Regev, Aviv</creator><creator>Goecks, Jeremy</creator><creator>Coffey, Robert J.</creator><creator>Coussens, Lisa M.</creator><creator>Santagata, Sandro</creator><creator>Sorger, Peter K.</creator><general>Nature Publishing Group US</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7SS</scope><scope>7TK</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-2389-1865</orcidid><orcidid>https://orcid.org/0000-0003-1359-4568</orcidid><orcidid>https://orcid.org/0000-0002-3364-1838</orcidid><orcidid>https://orcid.org/0000-0003-4702-7705</orcidid><orcidid>https://orcid.org/0000-0003-3293-3158</orcidid><orcidid>https://orcid.org/0000-0002-4583-5226</orcidid><orcidid>https://orcid.org/0000-0002-2180-3844</orcidid><orcidid>https://orcid.org/0000-0001-5724-1276</orcidid><orcidid>https://orcid.org/0000-0002-8056-0504</orcidid><orcidid>https://orcid.org/0000-0003-1144-5710</orcidid><orcidid>https://orcid.org/0000-0002-0811-637X</orcidid><orcidid>https://orcid.org/0000-0002-5196-3961</orcidid><orcidid>https://orcid.org/0000-0002-0299-3451</orcidid><orcidid>https://orcid.org/0000-0003-3776-1092</orcidid></search><sort><creationdate>20220301</creationdate><title>MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging</title><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></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-c1c70bf169bc9416d4babd1c57d1d466af3b7b7e9513fd057aa0c7967601aa13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>631/114/1564</topic><topic>631/114/794</topic><topic>631/553</topic><topic>Bioinformatics</topic><topic>Biological Microscopy</topic><topic>Biological Techniques</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedical Engineering/Biotechnology</topic><topic>Brief Communication</topic><topic>Computer applications</topic><topic>Diagnostic Imaging</topic><topic>Humans</topic><topic>Image acquisition</topic><topic>Image processing</topic><topic>Image Processing, Computer-Assisted - methods</topic><topic>Life Sciences</topic><topic>Multiplexing</topic><topic>Neoplasms - diagnostic imaging</topic><topic>Neoplasms - pathology</topic><topic>Proteomics</topic><topic>Software</topic><topic>Spatial analysis</topic><topic>Tissues</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schapiro, Denis</creatorcontrib><creatorcontrib>Sokolov, Artem</creatorcontrib><creatorcontrib>Yapp, Clarence</creatorcontrib><creatorcontrib>Chen, Yu-An</creatorcontrib><creatorcontrib>Muhlich, Jeremy L.</creatorcontrib><creatorcontrib>Hess, Joshua</creatorcontrib><creatorcontrib>Creason, Allison L.</creatorcontrib><creatorcontrib>Nirmal, Ajit J.</creatorcontrib><creatorcontrib>Baker, Gregory J.</creatorcontrib><creatorcontrib>Nariya, Maulik K.</creatorcontrib><creatorcontrib>Lin, Jia-Ren</creatorcontrib><creatorcontrib>Maliga, Zoltan</creatorcontrib><creatorcontrib>Jacobson, Connor A.</creatorcontrib><creatorcontrib>Hodgman, Matthew W.</creatorcontrib><creatorcontrib>Ruokonen, Juha</creatorcontrib><creatorcontrib>Farhi, Samouil L.</creatorcontrib><creatorcontrib>Abbondanza, Domenic</creatorcontrib><creatorcontrib>McKinley, Eliot T.</creatorcontrib><creatorcontrib>Persson, Daniel</creatorcontrib><creatorcontrib>Betts, Courtney</creatorcontrib><creatorcontrib>Sivagnanam, Shamilene</creatorcontrib><creatorcontrib>Regev, Aviv</creatorcontrib><creatorcontrib>Goecks, Jeremy</creatorcontrib><creatorcontrib>Coffey, Robert J.</creatorcontrib><creatorcontrib>Coussens, Lisa M.</creatorcontrib><creatorcontrib>Santagata, Sandro</creatorcontrib><creatorcontrib>Sorger, Peter K.</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schapiro, Denis</au><au>Sokolov, Artem</au><au>Yapp, Clarence</au><au>Chen, Yu-An</au><au>Muhlich, Jeremy L.</au><au>Hess, Joshua</au><au>Creason, Allison L.</au><au>Nirmal, Ajit J.</au><au>Baker, Gregory J.</au><au>Nariya, Maulik K.</au><au>Lin, Jia-Ren</au><au>Maliga, Zoltan</au><au>Jacobson, Connor A.</au><au>Hodgman, Matthew W.</au><au>Ruokonen, Juha</au><au>Farhi, Samouil L.</au><au>Abbondanza, Domenic</au><au>McKinley, Eliot T.</au><au>Persson, Daniel</au><au>Betts, Courtney</au><au>Sivagnanam, Shamilene</au><au>Regev, Aviv</au><au>Goecks, Jeremy</au><au>Coffey, Robert J.</au><au>Coussens, Lisa M.</au><au>Santagata, Sandro</au><au>Sorger, Peter K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging</atitle><jtitle>Nature methods</jtitle><stitle>Nat Methods</stitle><addtitle>Nat Methods</addtitle><date>2022-03-01</date><risdate>2022</risdate><volume>19</volume><issue>3</issue><spage>311</spage><epage>315</epage><pages>311-315</pages><issn>1548-7091</issn><issn>1548-7105</issn><eissn>1548-7105</eissn><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.
MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>34824477</pmid><doi>10.1038/s41592-021-01308-y</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0003-2389-1865</orcidid><orcidid>https://orcid.org/0000-0003-1359-4568</orcidid><orcidid>https://orcid.org/0000-0002-3364-1838</orcidid><orcidid>https://orcid.org/0000-0003-4702-7705</orcidid><orcidid>https://orcid.org/0000-0003-3293-3158</orcidid><orcidid>https://orcid.org/0000-0002-4583-5226</orcidid><orcidid>https://orcid.org/0000-0002-2180-3844</orcidid><orcidid>https://orcid.org/0000-0001-5724-1276</orcidid><orcidid>https://orcid.org/0000-0002-8056-0504</orcidid><orcidid>https://orcid.org/0000-0003-1144-5710</orcidid><orcidid>https://orcid.org/0000-0002-0811-637X</orcidid><orcidid>https://orcid.org/0000-0002-5196-3961</orcidid><orcidid>https://orcid.org/0000-0002-0299-3451</orcidid><orcidid>https://orcid.org/0000-0003-3776-1092</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1548-7091 |
| ispartof | Nature methods, 2022-03, Vol.19 (3), p.311-315 |
| issn | 1548-7091 1548-7105 1548-7105 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8916956 |
| source | MEDLINE; Nature Journals Online; SpringerLink Journals - AutoHoldings |
| subjects | 631/114/1564 631/114/794 631/553 Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Brief Communication Computer applications Diagnostic Imaging Humans Image acquisition Image processing Image Processing, Computer-Assisted - methods Life Sciences Multiplexing Neoplasms - diagnostic imaging Neoplasms - pathology Proteomics Software Spatial analysis Tissues Tumors |
| title | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-18T13%3A08%3A33IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=MCMICRO:%20a%20scalable,%20modular%20image-processing%20pipeline%20for%20multiplexed%20tissue%20imaging&rft.jtitle=Nature%20methods&rft.au=Schapiro,%20Denis&rft.date=2022-03-01&rft.volume=19&rft.issue=3&rft.spage=311&rft.epage=315&rft.pages=311-315&rft.issn=1548-7091&rft.eissn=1548-7105&rft_id=info:doi/10.1038/s41592-021-01308-y&rft_dat=%3Cproquest_pubme%3E2638176749%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2638176749&rft_id=info:pmid/34824477&rfr_iscdi=true |