Nature Methods

, volume 14 , issue 9 , pages 849-863

Data-analysis strategies for image-based cell profiling

Juan C. Caicedo ¹

Sam Cooper ²

Florian Heigwer ³

Scott Warchal ⁴

Peng Qiu ⁵

Csaba Molnár ⁶

Aliaksei S Vasilevich ⁷

Joseph D. Barry ⁸

Harmanjit Singh Bansal ⁹

Oren Kraus ¹⁰

Mathias Wawer ¹¹

Lassi Paavolainen ¹²

Markus D Herrmann ¹³

Mohammad Rohban ¹

Jane Hung ^{1, 14}

Holger Hennig ¹⁵

John Concannon ¹⁶

Ian Smith ¹⁷

Paul A Clemons ¹¹

Shantanu Singh ¹

Paul Rees ^{1, 18}

Peter Horvath ^{6, 12}

Roger G Linington ¹⁹

Anne E. Carpenter ¹

Hide authors affiliations Show authors affiliations: 19 affiliations

Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, USA |

IMPERIAL College London, London, UK |

German Cancer Research Center and Heidelberg University, Heidelberg, Germany

Heidelberg University

German Cancer Research Center

⁴

Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK |

⁵

Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA

Georgia Institute of technology

Emory University

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, USA |

⁹

National Centre for Biological Sciences, Bangalore, India |

¹⁰

Electrical and Computer Engineering, University of Toronto, Toronto, Canada |

¹¹

Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, USA |

¹²

Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland

University of Helsinki

Institute for Molecular Medicine Finland

¹³

Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland |

¹⁴

Department of Chemical Engineering, Massachusetts Institute Of Technology, Cambridge, 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, USA |

¹⁷

Connectivity Map Project, Broad Institute of Harvard and MIT, Cambridge, USA |

¹⁸

College of Engineering, Swansea University, Swansea, UK |

¹⁹

Department of Chemistry, Simon Fraser University, Burnaby, CANADA |

Publication type: Journal Article

Publication date: 2017-09-01

Springer Nature

Nature Methods

scimago Q1

wos Q1

SJR: 17.251

CiteScore: 49.0

Impact factor: 32.1

ISSN: 15487091, 15487105

DOI: 10.1038/nmeth.4397

Copy DOI

PubMed ID: 28858338

Biochemistry

Molecular Biology

Cell Biology

Biotechnology

Abstract

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.

Found

3 citations

Ohya Yoshikazu

29 publications, 490 citations, 1 review

h-index: 13

University of Tokyo

2 citations

Fukuzawa Hideya

PhD in Biological/biomedical sciences, professor

140 publications, 11 035 citations

1 citation

Tatout Christophe

49 publications, 1 713 citations, 7 reviews

h-index: 21

French Institute of Health and Medical Research

Université Clermont Auvergne

Research interests

Chromatin

Top-30

Journals

	5 10 15 20 25
Nature Communications	Nature Communications, 21, 3.22% Nature Communications 21 publications, 3.22%
bioRxiv	bioRxiv, 16, 2.45% bioRxiv 16 publications, 2.45%
Scientific Reports	Scientific Reports, 15, 2.3% Scientific Reports 15 publications, 2.3%
Nature Methods	Nature Methods, 9, 1.38% Nature Methods 9 publications, 1.38%
Cytometry. Part A : the journal of the International Society for Analytical Cytology	Cytometry. Part A : the journal of the International Society for Analytical Cytology, 9, 1.38% Cytometry. Part A : the journal of the International Society for Analytical Cytology 9 publications, 1.38%
Methods in Molecular Biology	Methods in Molecular Biology, 9, 1.38% Methods in Molecular Biology 9 publications, 1.38%
eLife	eLife, 9, 1.38% eLife 9 publications, 1.38%
SLAS Discovery	SLAS Discovery, 8, 1.23% SLAS Discovery 8 publications, 1.23%
PLoS ONE	PLoS ONE, 8, 1.23% PLoS ONE 8 publications, 1.23%
PLoS Computational Biology	PLoS Computational Biology, 8, 1.23% PLoS Computational Biology 8 publications, 1.23%
Communications Biology	Communications Biology, 7, 1.07% Communications Biology 7 publications, 1.07%
Lab on a Chip	Lab on a Chip, 7, 1.07% Lab on a Chip 7 publications, 1.07%
Bioinformatics	Bioinformatics, 7, 1.07% Bioinformatics 7 publications, 1.07%
Cell Systems	Cell Systems, 6, 0.92% Cell Systems 6 publications, 0.92%
Nature Protocols	Nature Protocols, 5, 0.77% Nature Protocols 5 publications, 0.77%
Science advances	Science advances, 5, 0.77% Science advances 5 publications, 0.77%
Journal of Cell Science	Journal of Cell Science, 4, 0.61% Journal of Cell Science 4 publications, 0.61%
BMC Bioinformatics	BMC Bioinformatics, 4, 0.61% BMC Bioinformatics 4 publications, 0.61%
Cell Reports Methods	Cell Reports Methods, 4, 0.61% Cell Reports Methods 4 publications, 0.61%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 4, 0.61% Computational and Structural Biotechnology Journal 4 publications, 0.61%
Trends in Biotechnology	Trends in Biotechnology, 4, 0.61% Trends in Biotechnology 4 publications, 0.61%
Toxicology and Applied Pharmacology	Toxicology and Applied Pharmacology, 4, 0.61% Toxicology and Applied Pharmacology 4 publications, 0.61%
Current Opinion in Chemical Biology	Current Opinion in Chemical Biology, 4, 0.61% Current Opinion in Chemical Biology 4 publications, 0.61%
Angewandte Chemie	Angewandte Chemie, 4, 0.61% Angewandte Chemie 4 publications, 0.61%
Angewandte Chemie - International Edition	Angewandte Chemie - International Edition, 4, 0.61% Angewandte Chemie - International Edition 4 publications, 0.61%
Lecture Notes in Computer Science	Lecture Notes in Computer Science, 4, 0.61% Lecture Notes in Computer Science 4 publications, 0.61%
Molecular Biology of the Cell	Molecular Biology of the Cell, 4, 0.61% Molecular Biology of the Cell 4 publications, 0.61%
Journal of Cell Biology	Journal of Cell Biology, 3, 0.46% Journal of Cell Biology 3 publications, 0.46%
Nature Reviews Methods Primers	Nature Reviews Methods Primers, 3, 0.46% Nature Reviews Methods Primers 3 publications, 0.46%
	5 10 15 20 25

Publishers

	20 40 60 80 100 120 140
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 136, 20.83% Cold Spring Harbor Laboratory 136 publications, 20.83%
Springer Nature	Springer Nature, 128, 19.6% Springer Nature 128 publications, 19.6%
Elsevier	Elsevier, 107, 16.39% Elsevier 107 publications, 16.39%
Wiley	Wiley, 55, 8.42% Wiley 55 publications, 8.42%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 22, 3.37% Royal Society of Chemistry (RSC) 22 publications, 3.37%
MDPI	MDPI, 20, 3.06% MDPI 20 publications, 3.06%
American Chemical Society (ACS)	American Chemical Society (ACS), 19, 2.91% American Chemical Society (ACS) 19 publications, 2.91%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 19, 2.91% Public Library of Science (PLoS) 19 publications, 2.91%
Institute of Electrical and Electronics Engineers (IEEE)	Institute of Electrical and Electronics Engineers (IEEE), 19, 2.91% Institute of Electrical and Electronics Engineers (IEEE) 19 publications, 2.91%
Frontiers Media S.A.	Frontiers Media S.A., 18, 2.76% Frontiers Media S.A. 18 publications, 2.76%
Oxford University Press	Oxford University Press, 13, 1.99% Oxford University Press 13 publications, 1.99%
SAGE	SAGE, 10, 1.53% SAGE 10 publications, 1.53%
eLife Sciences Publications	eLife Sciences Publications, 9, 1.38% eLife Sciences Publications 9 publications, 1.38%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 7, 1.07% American Association for the Advancement of Science (AAAS) 7 publications, 1.07%
The Company of Biologists	The Company of Biologists, 6, 0.92% The Company of Biologists 6 publications, 0.92%
IOP Publishing	IOP Publishing, 5, 0.77% IOP Publishing 5 publications, 0.77%
Taylor & Francis	Taylor & Francis, 4, 0.61% Taylor & Francis 4 publications, 0.61%
Rockefeller University Press	Rockefeller University Press, 4, 0.61% Rockefeller University Press 4 publications, 0.61%
American Association for Cancer Research (AACR)	American Association for Cancer Research (AACR), 4, 0.61% American Association for Cancer Research (AACR) 4 publications, 0.61%
American Society for Cell Biology (ASCB)	American Society for Cell Biology (ASCB), 4, 0.61% American Society for Cell Biology (ASCB) 4 publications, 0.61%
AIP Publishing	AIP Publishing, 3, 0.46% AIP Publishing 3 publications, 0.46%
American Society for Microbiology	American Society for Microbiology, 3, 0.46% American Society for Microbiology 3 publications, 0.46%
IGI Global	IGI Global, 3, 0.46% IGI Global 3 publications, 0.46%
Impact Journals	Impact Journals, 2, 0.31% Impact Journals 2 publications, 0.31%
Mary Ann Liebert	Mary Ann Liebert, 2, 0.31% Mary Ann Liebert 2 publications, 0.31%
Portland Press	Portland Press, 2, 0.31% Portland Press 2 publications, 0.31%
Hindawi Limited	Hindawi Limited, 2, 0.31% Hindawi Limited 2 publications, 0.31%
SPIE-Intl Soc Optical Eng	SPIE-Intl Soc Optical Eng, 2, 0.31% SPIE-Intl Soc Optical Eng 2 publications, 0.31%
Annual Reviews	Annual Reviews, 2, 0.31% Annual Reviews 2 publications, 0.31%
	20 40 60 80 100 120 140

We do not take into account publications without a DOI.
Statistics recalculated weekly.

Are you a researcher?

Create a profile to get free access to personal recommendations for colleagues and new articles.

Metrics

653

Cite this

GOST |

Cite this

GOST Copy

Caicedo J. C. et al. Data-analysis strategies for image-based cell profiling // Nature Methods. 2017. Vol. 14. No. 9. pp. 849-863.

GOST all authors (up to 50) Copy

Caicedo J. C., Cooper S., Heigwer F., Warchal S., Qiu P., Molnár C., Vasilevich A. S., Barry J. D., Bansal H. S., Kraus O., Wawer M., Paavolainen L., Herrmann M. D., Rohban M., Hung J., Hennig H., Concannon J., Smith I., Clemons P. A., Singh S., Rees P., Horvath P., Linington R. G., Carpenter A. E. Data-analysis strategies for image-based cell profiling // Nature Methods. 2017. Vol. 14. No. 9. pp. 849-863.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1038/nmeth.4397

UR - https://doi.org/10.1038/nmeth.4397

TI - Data-analysis strategies for image-based cell profiling

T2 - Nature Methods

AU - Caicedo, Juan C.

AU - Cooper, Sam

AU - Heigwer, Florian

AU - Warchal, Scott

AU - Qiu, Peng

AU - Molnár, Csaba

AU - Vasilevich, Aliaksei S

AU - Barry, Joseph D.

AU - Bansal, Harmanjit Singh

AU - Kraus, Oren

AU - Wawer, Mathias

AU - Paavolainen, Lassi

AU - Herrmann, Markus D

AU - Rohban, Mohammad

AU - Hung, Jane

AU - Hennig, Holger

AU - Concannon, John

AU - Smith, Ian

AU - Clemons, Paul A

AU - Singh, Shantanu

AU - Rees, Paul

AU - Horvath, Peter

AU - Linington, Roger G

AU - Carpenter, Anne E.

PY - 2017

DA - 2017/09/01

PB - Springer Nature

SP - 849-863

IS - 9

VL - 14

PMID - 28858338

SN - 1548-7091

SN - 1548-7105

ER -

BibTex |

Cite this

BibTex (up to 50 authors) Copy

@article{2017_Caicedo,

author = {Juan C. Caicedo and Sam Cooper and Florian Heigwer and Scott Warchal and Peng Qiu and Csaba Molnár and Aliaksei S Vasilevich and Joseph D. Barry and Harmanjit Singh Bansal and Oren Kraus and Mathias Wawer and Lassi Paavolainen and Markus D Herrmann and Mohammad Rohban and Jane Hung and Holger Hennig and John Concannon and Ian Smith and Paul A Clemons and Shantanu Singh and Paul Rees and Peter Horvath and Roger G Linington and Anne E. Carpenter},

title = {Data-analysis strategies for image-based cell profiling},

journal = {Nature Methods},

year = {2017},

volume = {14},

publisher = {Springer Nature},

month = {sep},

url = {https://doi.org/10.1038/nmeth.4397},

number = {9},

pages = {849--863},

doi = {10.1038/nmeth.4397}

}

MLA

Cite this

MLA Copy

Caicedo, Juan C., et al. “Data-analysis strategies for image-based cell profiling.” Nature Methods, vol. 14, no. 9, Sep. 2017, pp. 849-863. https://doi.org/10.1038/nmeth.4397.

Publisher

Springer Nature

Journal

Nature Methods

scimago Q1

wos Q1

SJR

17.251

CiteScore

49.0

Impact factor

32.1

ISSN

15487091 (Print)

15487105 (Electronic)