ABSTRACT
Tumors are complex assemblies of cellular and acellular structures patterned on spatial scales from microns to centimeters. Study of these assemblies has advanced dramatically with the introduction of methods for highly multiplexed tissue imaging methods. These reveal the intensities and spatial distributions of 20-100 proteins in 103–107 cells per specimen in a preserved tissue microenvironment. Despite extensive work on extracting single-cell image data, all tissue images are afflicted by artifacts (e.g., folds, debris, antibody aggregates, optical effects, image processing errors) that arise from imperfections in specimen preparation, data acquisition, image assembly, and feature extraction. We show that artifacts dramatically impact single-cell data analysis, in extreme cases, preventing meaningful biological interpretation. We describe an interactive quality control software tool, CyLinter, that identifies and removes data associated with imaging artifacts. CyLinter greatly improves single-cell analysis, especially for archival specimens sectioned many years prior to data collection, including those from clinical trials.
Competing Interest Statement
P.K.S. is a cofounder and member of the Board of Directors of Glencoe Software, a member of the Board of Directors for Applied Biomath and a member of the Scientific Advisory Board for RareCyte, NanoString and Montai Health; he holds equity in Glencoe, Applied Biomath and RareCyte. P.K.S. is a consultant for Merck, and the Sorger lab has received research funding from Novartis and Merck in the past 5 years. PKS declares that none of these relationships have influenced the content of this manuscript. E. A. M. reports compensated service on Scientific Advisory Boards for Astra Zeneca, BioNTech and Merck, uncompensated service on Steering Committees for Bristol Myers Squibb and Roche/Genentech; speakers' honoraria and travel support from Merck Sharp & Dohme; and institutional research support from Roche/Genentech (via an SU2C grant) and Gilead. She also reports research funding from Susan Komen for the Cure for which she serves as a Scientific Advisor, and uncompensated participation as a member of the American Society of Clinical Oncology Board of Directors. J. L. G. serves or has previously served on advisory boards and/or as a scientific advisory board member for Array BioPharma/Pfizer, AstraZeneca, BD Biosciences, Carisma, Codagenix, Duke Street Bio, GlaxoSmithKline, Kowa, Kymera, OncoOne and Verseau Therapeutics, and has research grants from Array BioPharma/Pfizer, Duke Street Bio, Eli Lilly, GlaxoSmithKline and Merck. The other authors declare no competing interests.
