A cell-level quality control workflow for high-throughput image analysis

• Published in: BMC bioinformatics Vol. 21; no. 1; pp. 1 - 280
• Main Authors: Qiu, Minhua, Zhou, Bin, Lo, Frederick, Cook, Steven, Chyba, Jason, Quackenbush, Doug, Matzen, Jason, Li, Zhizhong, Mak, Puiying Annie, Chen, Kaisheng, Zhou, Yingyao
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 02-07-2020; BioMed Central; BMC
• Subjects: Algorithms; Assaying; Cell-level quality control; CellProfiler; Clustering; Gating; Genotype & phenotype; High throughput image analysis; Image analysis; Image classification; Image processing; Image processing equipment; Image quality; Image quality measurement; Image segmentation; Information management; Inspection; Learning algorithms; Machine learning; Methodology; Phenotypes; Phenotypic variations; Quality assessment; Quality control; Quality management; Rankings; Staining; Support vector machines; Thresholds; Workflow; Workflow software
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-020-03603-5

Image-based high throughput (HT) screening provides a rich source of information on dynamic cellular response to external perturbations. The large quantity of data generated necessitates computer-aided quality control (QC) methodologies to flag imaging and staining artifacts. Existing image- or patch-level QC methods require separate thresholds to be simultaneously tuned for each image quality metric used, and also struggle to distinguish between artifacts and valid cellular phenotypes. As a result, extensive time and effort must be spent on per-assay QC feature thresholding, and valid images and phenotypes may be discarded while image- and cell-level artifacts go undetected. We present a novel cell-level QC workflow built on machine learning approaches for classifying artifacts from HT image data. First, a phenotype sampler based on unlabeled clustering collects a comprehensive subset of cellular phenotypes, requiring only the inspection of a handful of images per phenotype for validity. A set of one-class support vector machines are then trained on each biologically valid image phenotype, and used to classify individual objects in each image as valid cells or artifacts. We apply this workflow to two real-world large-scale HT image datasets and observe that the ratio of artifact to total object area (AR.sub.cell) provides a single robust assessment of image quality regardless of the underlying causes of quality issues. Gating on this single intuitive metric, partially contaminated images can be salvaged and highly contaminated images can be excluded before image-level phenotype summary, enabling a more reliable characterization of cellular response dynamics. Our cell-level QC workflow enables identification of artificial cells created not only by staining or imaging artifacts but also by the limitations of image segmentation algorithms. The single readout AR.sub.cell that summaries the ratio of artifacts contained in each image can be used to reliably rank images by quality and more accurately determine QC cutoff thresholds. Machine learning-based cellular phenotype clustering and sampling reduces the amount of manual work required for training example collection. Our QC workflow automatically handles assay-specific phenotypic variations and generalizes to different HT image assays.