Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images
Multiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage of signals in densely packed tissues presents an obstacle to the assignment of high-dimensional spatial features to individual cells for accurate...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-07-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2021.652631/full |
| _version_ | 1818741061838700544 |
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| author | Yunhao Bai Yunhao Bai Bokai Zhu Bokai Zhu Xavier Rovira-Clave Han Chen Maxim Markovic Chi Ngai Chan Tung-Hung Su Tung-Hung Su David R. McIlwain Jacob D. Estes Leeat Keren Leeat Keren Garry P. Nolan Sizun Jiang Sizun Jiang |
| author_facet | Yunhao Bai Yunhao Bai Bokai Zhu Bokai Zhu Xavier Rovira-Clave Han Chen Maxim Markovic Chi Ngai Chan Tung-Hung Su Tung-Hung Su David R. McIlwain Jacob D. Estes Leeat Keren Leeat Keren Garry P. Nolan Sizun Jiang Sizun Jiang |
| author_sort | Yunhao Bai |
| collection | DOAJ |
| description | Multiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage of signals in densely packed tissues presents an obstacle to the assignment of high-dimensional spatial features to individual cells for accurate cell-type annotation. We devised a method to correct for lateral spillage of cell surface markers between adjacent cells termed REinforcement Dynamic Spillover EliminAtion (REDSEA). The use of REDSEA decreased contaminating signals from neighboring cells. It improved the recovery of marker signals across both isotopic (i.e., Multiplexed Ion Beam Imaging) and immunofluorescent (i.e., Cyclic Immunofluorescence) multiplexed images resulting in a marked improvement in cell-type classification. |
| first_indexed | 2024-12-18T01:50:38Z |
| format | Article |
| id | doaj.art-a231bbf0fefd4cca83ac3f75a764e8ae |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-18T01:50:38Z |
| publishDate | 2021-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-a231bbf0fefd4cca83ac3f75a764e8ae2022-12-21T21:25:03ZengFrontiers Media S.A.Frontiers in Immunology1664-32242021-07-011210.3389/fimmu.2021.652631652631Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed ImagesYunhao Bai0Yunhao Bai1Bokai Zhu2Bokai Zhu3Xavier Rovira-Clave4Han Chen5Maxim Markovic6Chi Ngai Chan7Tung-Hung Su8Tung-Hung Su9David R. McIlwain10Jacob D. Estes11Leeat Keren12Leeat Keren13Garry P. Nolan14Sizun Jiang15Sizun Jiang16Department of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Chemistry, Stanford University, Stanford, CA, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesVaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Internal Medicine, National Taiwan University Hospital, Taipei, TaiwanDepartment of Pathology, Stanford University, Stanford, CA, United StatesVaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, IsraelDepartment of Pathology, Stanford University, Stanford, CA, United StatesDepartment of Pathology, Stanford University, Stanford, CA, United StatesCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United StatesMultiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage of signals in densely packed tissues presents an obstacle to the assignment of high-dimensional spatial features to individual cells for accurate cell-type annotation. We devised a method to correct for lateral spillage of cell surface markers between adjacent cells termed REinforcement Dynamic Spillover EliminAtion (REDSEA). The use of REDSEA decreased contaminating signals from neighboring cells. It improved the recovery of marker signals across both isotopic (i.e., Multiplexed Ion Beam Imaging) and immunofluorescent (i.e., Cyclic Immunofluorescence) multiplexed images resulting in a marked improvement in cell-type classification.https://www.frontiersin.org/articles/10.3389/fimmu.2021.652631/fullmultiplexed tissue imagingspatial proteomicssignal spilloverimage correctionsingle-cell biologycell annotation |
| spellingShingle | Yunhao Bai Yunhao Bai Bokai Zhu Bokai Zhu Xavier Rovira-Clave Han Chen Maxim Markovic Chi Ngai Chan Tung-Hung Su Tung-Hung Su David R. McIlwain Jacob D. Estes Leeat Keren Leeat Keren Garry P. Nolan Sizun Jiang Sizun Jiang Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images Frontiers in Immunology multiplexed tissue imaging spatial proteomics signal spillover image correction single-cell biology cell annotation |
| title | Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images |
| title_full | Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images |
| title_fullStr | Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images |
| title_full_unstemmed | Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images |
| title_short | Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images |
| title_sort | adjacent cell marker lateral spillover compensation and reinforcement for multiplexed images |
| topic | multiplexed tissue imaging spatial proteomics signal spillover image correction single-cell biology cell annotation |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2021.652631/full |
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