@article{992227ae38654865bb83ed3e10a02039,
title = "Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms",
abstract = "The emergence of megascale single-cell multiplex tissue imaging (MTI) datasets necessitates reproducible, scalable, and robust tools for cell phenotyping and spatial analysis. We developed open-source, graphics processing unit (GPU)-accelerated tools for intensity normalization, phenotyping, and microenvironment characterization. We deploy the toolkit on a human breast cancer (BC) tissue microarray stained by cyclic immunofluorescence and present the first cross-validation of breast cancer cell phenotypes derived by using two different MTI platforms. Finally, we demonstrate an integrative phenotypic and spatial analysis revealing BC subtype-specific features.",
keywords = "GPU data science, breast cancer, image analytics, multiplex tissue imaging, systems biology",
author = "Burlingame, {Erik A.} and Jennifer Eng and Guillaume Thibault and Koei Chin and Gray, {Joe W.} and Chang, {Young Hwan}",
note = "Funding Information: This work was supported in part by the National Cancer Institute ( U54CA209988 , U2CCA233280 , U01 CA224012 , R01 CA253860 ), CRUK -OHSU joint funding award, the OHSU Center for Spatial Systems Biomedicine , and a Biomedical Innovation Program Award from the Oregon Clinical and Translational Research Institute . We acknowledge expert technical assistance by staff in the Advanced Multiscale Microscopy Shared Resource, supported by the OHSU Knight Cancer Institute ( NIH P30 CA069533 ) and the Office of the Senior Vice President for Research. Equipment purchases included support by the OHSU Center for Spatial Systems Biomedicine, the MJ Murdock Charitable Trust , and the Collins Foundation . We also acknowledge Mitchell Dowsett for his contribution of TMAs used in this study. The resources of the Exacloud high-performance computing environment developed jointly by OHSU and Intel and the technical support of the OHSU Advanced Computing Center are gratefully acknowledged. E.A.B. receives support from a scholar award provided by the ARCS (Achievement Rewards for College Scientists) Foundation Oregon. Funding Information: This work was supported in part by the National Cancer Institute (U54CA209988, U2CCA233280, U01 CA224012, R01 CA253860), CRUK-OHSU joint funding award, the OHSU Center for Spatial Systems Biomedicine, and a Biomedical Innovation Program Award from the Oregon Clinical and Translational Research Institute. We acknowledge expert technical assistance by staff in the Advanced Multiscale Microscopy Shared Resource, supported by the OHSU Knight Cancer Institute (NIH P30 CA069533) and the Office of the Senior Vice President for Research. Equipment purchases included support by the OHSU Center for Spatial Systems Biomedicine, the MJ Murdock Charitable Trust, and the Collins Foundation. We also acknowledge Mitchell Dowsett for his contribution of TMAs used in this study. The resources of the Exacloud high-performance computing environment developed jointly by OHSU and Intel and the technical support of the OHSU Advanced Computing Center are gratefully acknowledged. E.A.B. receives support from a scholar award provided by the ARCS (Achievement Rewards for College Scientists) Foundation Oregon. Conceptualization, E.A.B. J.W.G. and Y.H.C.; methodology, E.A.B. J.E. G.T. K.C. J.W.G. and Y.H.C.; software, E.A.B. G.T. and Y.H.C.; validation, E.A.B. J.E. K.C. and Y.H.C.; formal analysis, E.A.B.; investigation, E.A.B. and J.E.; resources, K.C. and J.W.G.; data curation, E.A.B. and J.E.; writing ? original draft, E.A.B. and Y.H.C.; Writing ? review & editing, E.A.B. J.W.G. and Y.H.C.; visualization, E.A.B.; supervision, J.W.G. and Y.H.C.; project administration, J.W.G. and Y.H.C.; funding acquisition, E.A.B. Y.H.C. and J.W.G. J.W.G. has licensed technologies to Abbott Diagnostics; has ownership positions in Convergent Genomics, Health Technology Innovations, Zorro Bio, and PDX Pharmaceuticals; serves as a paid consultant to New Leaf Ventures; has received research support from Thermo Fisher Scientific (formerly FEI), Zeiss, Miltenyi Biotech, Quantitative Imaging, Health Technology Innovations, and Micron Technologies; and owns stock in Abbott Diagnostics, AbbVie, Alphabet, Amazon, Amgen, Apple, General Electric, Gilead, Intel, Microsoft, Nvidia, and Zimmer Biomet. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = aug,
day = "23",
doi = "10.1016/j.crmeth.2021.100053",
language = "English (US)",
volume = "1",
journal = "Cell Reports Methods",
issn = "2667-2375",
publisher = "Cell Press",
number = "4",
}