Data-analysis strategies for image-based cell profiling

• Published in: Nature methods Vol. 14; no. 9; pp. 849 - 863
• Main Authors: Caicedo, Juan C, Cooper, Sam, Heigwer, Florian, Warchal, Scott, Qiu, Peng, Molnar, Csaba, Vasilevich, Aliaksei S, Barry, Joseph D, Bansal, Harmanjit Singh, Kraus, Oren, Wawer, Mathias, Paavolainen, Lassi, Herrmann, Markus D, Rohban, Mohammad, Hung, Jane, Hennig, Holger, Concannon, John, Smith, Ian, Clemons, Paul A, Singh, Shantanu, Rees, Paul, Horvath, Peter, Linington, Roger G, Carpenter, Anne E
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2017; Nature Publishing Group
• Subjects: 631/114/1305; 631/114/1564; Algorithms; Animals; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; Cell Tracking - methods; Data analysis; Data Interpretation, Statistical; Data processing; High-Throughput Screening Assays - methods; Humans; Image acquisition; Image Interpretation, Computer-Assisted - methods; Image processing; Image quality; Laboratories; Laboratory tests; Life Sciences; Machine Learning; Methods; Microscopy; Microscopy - methods; Organic chemistry; Pattern Recognition, Automated - methods; Proteomics; review-article; Tissue Array Analysis - methods; Workflow; Canada; United States
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/nmeth.4397

This Review covers the steps required to create high-quality image-based profiles from high-throughput microscopy images. Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.