Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images

Yunhao Bai; Bokai Zhu; Xavier Rovira-Clave; Han Chen; Maxim Markovic; Chi Ngai Chan; Tung Hung Su; David R. McIlwain; Jacob D. Estes; Leeat Keren; Garry P. Nolan; Sizun Jiang

doi:10.3389/fimmu.2021.652631

Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images

Yunhao Bai, Bokai Zhu, Xavier Rovira-Clave, Han Chen, Maxim Markovic, Chi Ngai Chan, Tung Hung Su, David R. McIlwain, Jacob D. Estes, Leeat Keren, Garry P. Nolan, Sizun Jiang

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

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.

Original language	English (US)
Article number	652631
Journal	Frontiers in immunology
Volume	12
DOIs	https://doi.org/10.3389/fimmu.2021.652631
State	Published - Jul 5 2021

Keywords

cell annotation
image correction
multiplexed tissue imaging
signal spillover
single-cell biology
spatial proteomics

ASJC Scopus subject areas

Immunology and Allergy
Immunology

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10.3389/fimmu.2021.652631

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title = "Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images",

abstract = "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.",

keywords = "cell annotation, image correction, multiplexed tissue imaging, signal spillover, single-cell biology, spatial proteomics",

author = "Yunhao Bai and Bokai Zhu and Xavier Rovira-Clave and Han Chen and Maxim Markovic and Chan, {Chi Ngai} and Su, {Tung Hung} and McIlwain, {David R.} and Estes, {Jacob D.} and Leeat Keren and Nolan, {Garry P.} and Sizun Jiang",

note = "Publisher Copyright: {\textcopyright} Copyright {\textcopyright} 2021 Bai, Zhu, Rovira-Clave, Chen, Markovic, Chan, Su, McIlwain, Estes, Keren, Nolan and Jiang.",

year = "2021",

month = jul,

day = "5",

doi = "10.3389/fimmu.2021.652631",

language = "English (US)",

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AU - Bai, Yunhao

AU - Zhu, Bokai

AU - Rovira-Clave, Xavier

AU - Chen, Han

AU - Markovic, Maxim

AU - Chan, Chi Ngai

AU - Su, Tung Hung

AU - McIlwain, David R.

AU - Estes, Jacob D.

AU - Keren, Leeat

AU - Nolan, Garry P.

AU - Jiang, Sizun

PY - 2021/7/5

Y1 - 2021/7/5

N2 - 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.

AB - 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.

KW - cell annotation

KW - image correction

KW - multiplexed tissue imaging

KW - signal spillover

KW - single-cell biology

KW - spatial proteomics

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Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images

Abstract

Keywords

ASJC Scopus subject areas

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