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ColonyArea specifications


Unique identifier OMICS_25409
Name ColonyArea
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 01
Stability Stable
Maintained Yes




No version available



  • person_outline Daniel Abankwa

Publication for ColonyArea

ColonyArea citations


Antitumor activity of the polo like kinase inhibitor, TAK 960, against preclinical models of colorectal cancer

BMC Cancer
PMCID: 5800287
PMID: 29402316
DOI: 10.1186/s12885-018-4036-z

[…] visible colonies in doses of TAK-960 greater than 10 nM (Fig. ). The decrease in colony growth was evaluated qualitatively by a visual decrease in crystal violet stain and quantitatively by Image J (ColonyArea plugin). Colony formation of CRC cell lines DLD1 and COLO678 decreased dose dependently, however, < 10% area coverage occurred at TAK-960 levels greater than 20 nM. In all CRC cell lines, t […]


The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability

Nucleic Acids Res
PMCID: 5861405
PMID: 29361176
DOI: 10.1093/nar/gky008

[…] mperature. The crystal violet solution was removed by rinsing plates in tap water and the plates were allowed to air dry overnight. Plates were then imaged on a flatbed scanner and analyzed using the ColonyArea plugin for ImageJ (). […]


Extreme sensitivity to ultraviolet light in the fungal pathogen causing white nose syndrome of bats

Nat Commun
PMCID: 5750222
PMID: 29295979
DOI: 10.1038/s41467-017-02441-z

[…] athogenic Pseudogymnoascus species were incubated for 7 days, while P. destructans was incubated for 14 days. The plates were then photographed and growth was quantified using the Fiji/ImageJ plug-in ColonyArea 1.5. Relative growth was then normalized to growth on glucose and plotted in heatmap.2 from the gplots package in R. […]


PARP inhibition causes premature loss of cohesion in cancer cells

PMCID: 5732777
PMID: 29262611
DOI: 10.18632/oncotarget.21879

[…] and dishes were washed in filtered water until residual crystal violet was completely removed. Percentage of surviving cells was quantified by measuring the area of colonies using the ImageJ-plugin ‘ColonyArea’. The intensity of colonies was not taken into account due to variable staining of different cell lines by crystal violet. The quantification is based on at least two independent experiment […]


DNA repair factor RAD18 and DNA polymerase Polκ confer tolerance of oncogenic DNA replication stress

PMCID: 5626543
PMID: 28835467
DOI: 10.1083/jcb.201702006

[…] medium. Growth medium was replenished every 3 d. Colonies containing ∼50 surviving cells were stained with 0.05% crystal violet in 1× PBS containing 1% methanol and 1% formaldehyde. The ImageJ plugin ColonyArea () was used to automatically quantify stained colonies. In some experiments, lentivirally expressed sgRNAs were used to functionally inactivate PolQ and Brca1 genes exactly as described pre […]


Novel galeterone analogs act independently of AR and AR V7 for the activation of the unfolded protein response and induction of apoptosis in the CWR22Rv1 prostate cancer cell model

PMCID: 5687622
PMID: 29179452
DOI: 10.18632/oncotarget.19762

[…] ). Images of the 6-well plates were generated using a digital scanner. Colonies were manually counted (>30 cells) and total colony area was calculated using ImageJ software with “Colony Counter” and “ColonyArea” plugins. Representative images and plots of the mean ± standard deviation of treated groups versus vehicle controls are shown. Statistical analysis was performed using Student’s t test and […]


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ColonyArea institution(s)
Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, Finland; Department of Pathology, University of Turku, Turku, Finland; Turku Doctoral Program of Biomedical Sciences, University of Turku and Abo Akademi University, Turku, Finland
ColonyArea funding source(s)
Supported by the Academy of Finland fellowship grant, the Sigrid Juselius Foundation, the Cancer Society of Finland and the Marie-Curie Reintegration Grant and by the Foundation of the Finnish Cancer Institute and the Sigrid Juselius Foundation.

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