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Nat Methods. 2017 Aug 31;14(9):849-863. doi: 10.1038/nmeth.4397.

Data-analysis strategies for image-based cell profiling.

Author information

1
Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
2
Imperial College London, London, UK.
3
German Cancer Research Center and Heidelberg University, Heidelberg, Germany.
4
Institute of Genetics &Molecular Medicine, University of Edinburgh, Edinburgh, UK.
5
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA.
6
Synthetic and System Biology Unit, Hungarian Academy of Sciences, Szeged, Hungary.
7
Laboratory for Cell Biology-Inspired Tissue Engineering, MERLN Institute, Maastricht University, Maastricht, the Netherlands.
8
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
9
National Centre for Biological Sciences, Bangalore, India.
10
Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada.
11
Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
12
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
13
Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
14
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
15
Department of Systems Biology &Bioinformatics, University of Rostock, Rostock, Germany.
16
Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA.
17
Connectivity Map Project, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
18
College of Engineering, Swansea University, Swansea, UK.
19
Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

Abstract

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.

PMID:
28858338
DOI:
10.1038/nmeth.4397
[Indexed for MEDLINE]

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