Open Access

PLoS ONE, volume 9, issue 3, pages e92444

ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays

Guzmán Camilo ¹

Bagga Manish ¹

Kaur Amanpreet ²

Westermarck Jukka ²

Abankwa Daniel ¹

Hide authors affiliations Show authors affiliations: 2 affiliations

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland

Åbo Akademi University

Turku Centre for Biotechnology

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland,

Åbo Akademi University

Turku Centre for Biotechnology

Publication type: Journal Article

Publication date: 2014-03-19

Public Library of Science (PLoS)

Journal: PLoS ONE

Quartile SCImago

Quartile WOS

Impact factor: 3.7

ISSN: 19326203

DOI: 10.1371/journal.pone.0092444

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PubMed ID: 24647355

Multidisciplinary

Abstract

The clonogenic or colony formation assay is a widely used method to study the number and size of cancer cell colonies that remain after irradiation or cytotoxic agent administration and serves as a measure for the anti-proliferative effect of these treatments. Alternatively, this assay is used to quantitate the transforming potential of cancer associated genes and chemical agents. Therefore, there is a need for a simplified and standardized analysis of colony formation assays for both routine laboratory use and for parallelized automated analysis. Here we describe the freely available ImageJ-plugin “ColonyArea”, which is optimized for rapid and quantitative analysis of focus formation assays conducted in 6- to 24-well dishes. ColonyArea processes image data of multi-well dishes, by separating, concentrically cropping and background correcting well images individually, before colony formation is quantitated. Instead of counting the number of colonies, ColonyArea determines the percentage of area covered by crystal violet stained cell colonies, also taking the intensity of the staining and therefore cell density into account. We demonstrate that these parameters alone or in combination allow for robust quantification of IC50 values of the cytotoxic effect of two staurosporines, UCN-01 and staurosporine (STS) on human glioblastoma cells (T98G). The relation between the potencies of the two compounds compared very well with that obtained from an absorbance based method to quantify colony growth and to published data. The ColonyArea ImageJ plugin provides a simple and efficient analysis routine to quantitate assay data of one of the most commonly used cellular assays. The bundle is freely available for download as supporting information. We expect that ColonyArea will be of broad utility for cancer biologists, as well as clinical radiation scientists.

By date By citations

Citations by journals

	2 4 6 8 10 12 14 16 18 20
Cancers	Cancers, 19, 4.2% Cancers 19 publications, 4.2%
Scientific Reports	Scientific Reports, 16, 3.54% Scientific Reports 16 publications, 3.54%
Oncotarget	Oncotarget, 11, 2.43% Oncotarget 11 publications, 2.43%
PLoS ONE	PLoS ONE, 11, 2.43% PLoS ONE 11 publications, 2.43%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 9, 1.99% International Journal of Molecular Sciences 9 publications, 1.99%
Nature Communications	Nature Communications, 9, 1.99% Nature Communications 9 publications, 1.99%
Molecular Oncology	Molecular Oncology, 8, 1.77% Molecular Oncology 8 publications, 1.77%
Cells	Cells, 7, 1.55% Cells 7 publications, 1.55%
Cell Reports	Cell Reports, 7, 1.55% Cell Reports 7 publications, 1.55%
Frontiers in Oncology	Frontiers in Oncology, 6, 1.33% Frontiers in Oncology 6 publications, 1.33%
Oncogene	Oncogene, 6, 1.33% Oncogene 6 publications, 1.33%
Journal of Biological Chemistry	Journal of Biological Chemistry, 6, 1.33% Journal of Biological Chemistry 6 publications, 1.33%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 6, 1.33% Proceedings of the National Academy of Sciences of the United States of America 6 publications, 1.33%
Cancer Research	Cancer Research, 5, 1.11% Cancer Research 5 publications, 1.11%
Molecular Cancer Therapeutics	Molecular Cancer Therapeutics, 5, 1.11% Molecular Cancer Therapeutics 5 publications, 1.11%
eLife	eLife, 5, 1.11% eLife 5 publications, 1.11%
Pharmaceuticals	Pharmaceuticals, 4, 0.88% Pharmaceuticals 4 publications, 0.88%
BMC Cancer	BMC Cancer, 4, 0.88% BMC Cancer 4 publications, 0.88%
Life Sciences	Life Sciences, 4, 0.88% Life Sciences 4 publications, 0.88%
Science advances	Science advances, 4, 0.88% Science advances 4 publications, 0.88%
FASEB Journal	FASEB Journal, 4, 0.88% FASEB Journal 4 publications, 0.88%
Journal of Natural Products	Journal of Natural Products, 4, 0.88% Journal of Natural Products 4 publications, 0.88%
Cancer Discovery	Cancer Discovery, 4, 0.88% Cancer Discovery 4 publications, 0.88%
Molecular Cancer Research	Molecular Cancer Research, 4, 0.88% Molecular Cancer Research 4 publications, 0.88%
Frontiers in Pharmacology	Frontiers in Pharmacology, 3, 0.66% Frontiers in Pharmacology 3 publications, 0.66%
Cell Death and Disease	Cell Death and Disease, 3, 0.66% Cell Death and Disease 3 publications, 0.66%
Frontiers in Cell and Developmental Biology	Frontiers in Cell and Developmental Biology, 3, 0.66% Frontiers in Cell and Developmental Biology 3 publications, 0.66%
Cell Death and Differentiation	Cell Death and Differentiation, 3, 0.66% Cell Death and Differentiation 3 publications, 0.66%
Molecular Cell	Molecular Cell, 3, 0.66% Molecular Cell 3 publications, 0.66%
	2 4 6 8 10 12 14 16 18 20

Citations by publishers

	10 20 30 40 50 60 70 80
Springer Nature	Springer Nature, 78, 17.26% Springer Nature 78 publications, 17.26%
Elsevier	Elsevier, 76, 16.81% Elsevier 76 publications, 16.81%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 49, 10.84% Multidisciplinary Digital Publishing Institute (MDPI) 49 publications, 10.84%
Wiley	Wiley, 32, 7.08% Wiley 32 publications, 7.08%
American Association for Cancer Research (AACR)	American Association for Cancer Research (AACR), 23, 5.09% American Association for Cancer Research (AACR) 23 publications, 5.09%
Frontiers Media S.A.	Frontiers Media S.A., 16, 3.54% Frontiers Media S.A. 16 publications, 3.54%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 15, 3.32% Public Library of Science (PLoS) 15 publications, 3.32%
American Chemical Society (ACS)	American Chemical Society (ACS), 12, 2.65% American Chemical Society (ACS) 12 publications, 2.65%
Impact Journals	Impact Journals, 11, 2.43% Impact Journals 11 publications, 2.43%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 7, 1.55% American Society for Biochemistry and Molecular Biology 7 publications, 1.55%
Oxford University Press	Oxford University Press, 6, 1.33% Oxford University Press 6 publications, 1.33%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 6, 1.33% Proceedings of the National Academy of Sciences (PNAS) 6 publications, 1.33%
Spandidos Publications	Spandidos Publications, 5, 1.11% Spandidos Publications 5 publications, 1.11%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 5, 1.11% American Association for the Advancement of Science (AAAS) 5 publications, 1.11%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 5, 1.11% Royal Society of Chemistry (RSC) 5 publications, 1.11%
eLife Sciences Publications	eLife Sciences Publications, 5, 1.11% eLife Sciences Publications 5 publications, 1.11%
Federation of American Societies for Experimental Biology (FASEB)	Federation of American Societies for Experimental Biology (FASEB), 4, 0.88% Federation of American Societies for Experimental Biology (FASEB) 4 publications, 0.88%
Taylor & Francis	Taylor & Francis, 3, 0.66% Taylor & Francis 3 publications, 0.66%
EMBO press	EMBO press, 3, 0.66% EMBO press 3 publications, 0.66%
American Society for Microbiology	American Society for Microbiology, 3, 0.66% American Society for Microbiology 3 publications, 0.66%
Rockefeller University Press	Rockefeller University Press, 3, 0.66% Rockefeller University Press 3 publications, 0.66%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 3, 0.66% Cold Spring Harbor Laboratory 3 publications, 0.66%
The Company of Biologists	The Company of Biologists, 2, 0.44% The Company of Biologists 2 publications, 0.44%
Mary Ann Liebert	Mary Ann Liebert, 2, 0.44% Mary Ann Liebert 2 publications, 0.44%
SAGE	SAGE, 2, 0.44% SAGE 2 publications, 0.44%
IOP Publishing	IOP Publishing, 2, 0.44% IOP Publishing 2 publications, 0.44%
Dove Medical Press	Dove Medical Press, 2, 0.44% Dove Medical Press 2 publications, 0.44%
BMJ	BMJ, 2, 0.44% BMJ 2 publications, 0.44%
American Society for Clinical Investigation	American Society for Clinical Investigation, 1, 0.22% American Society for Clinical Investigation 1 publication, 0.22%
	10 20 30 40 50 60 70 80

We do not take into account publications that without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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Guzmán C. et al. ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays // PLoS ONE. 2014. Vol. 9. No. 3. p. e92444.

GOST all authors (up to 50) Copy

Guzmán C., Bagga M., Kaur A., Westermarck J., Abankwa D. ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays // PLoS ONE. 2014. Vol. 9. No. 3. p. e92444.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1371/journal.pone.0092444

UR - https://doi.org/10.1371%2Fjournal.pone.0092444

TI - ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays

T2 - PLoS ONE

AU - Guzmán, Camilo

AU - Bagga, Manish

AU - Kaur, Amanpreet

AU - Westermarck, Jukka

AU - Abankwa, Daniel

PY - 2014

DA - 2014/03/19 00:00:00

PB - Public Library of Science (PLoS)

SP - e92444

IS - 3

VL - 9

PMID - 24647355

SN - 1932-6203

ER -

BibTex |

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BibTex Copy

@article{2014_Guzmán,

author = {Camilo Guzmán and Manish Bagga and Amanpreet Kaur and Jukka Westermarck and Daniel Abankwa},

title = {ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays},

journal = {PLoS ONE},

year = {2014},

volume = {9},

publisher = {Public Library of Science (PLoS)},

month = {mar},

url = {https://doi.org/10.1371%2Fjournal.pone.0092444},

number = {3},

pages = {e92444},

doi = {10.1371/journal.pone.0092444}

}

MLA

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MLA Copy

Guzmán, Camilo, et al. “ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays.” PLoS ONE, vol. 9, no. 3, Mar. 2014, p. e92444. https://doi.org/10.1371%2Fjournal.pone.0092444.

Found error?

Publisher

Public Library of Science (PLoS)

Journal

PLoS ONE

Quartile SCImago

Quartile WOS

Impact factor

3.7

ISSN

19326203 (Print)