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OpenCFU specifications


Unique identifier OMICS_14951
Name OpenCFU
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Medium
Version 3.9.0
Stability Stable
Maintained Yes




No version available



  • person_outline Quentin Geissmann <>

Publication for OpenCFU

OpenCFU citations


Rapid Gene Concatenation for Genetic Rescue of Multigene Mutants in Candida albicans

PMCID: 5917427
PMID: 29695626
DOI: 10.1128/mSphere.00169-18

[…] an aliquot of cells was then imaged using conventional fluorescence microscopy on a zeiss axio observer z.1 fluorescence microscope and a 20× 0.8-na objective., colony counts were collected using opencfu software (). microscopy images were compiled with imagej (), photoshop cs6, and microsoft powerpoint 2010. rna counts were analyzed in microsoft excel 2010 and graphpad prism 7. heat maps […]


The clinicopathological significance of monocarboxylate transporters in testicular germ cell tumors

PMCID: 5945514
PMID: 29755659
DOI: 10.18632/oncotarget.24910

[…] cells were fixed with methanol and stained with hematoxylin and eosin for 10 min. membranes were photographed in olympus bx43 (×10 magnification), and migrating cells were counted using the opencfu software (version 3.8) []. results are represented as percentage of cell migration normalized for the control condition, of two independent experiments in duplicate., invasion capacity […]


Interplay between RNASEH2 and MOV10 controls LINE 1 retrotransposition

PMCID: 5829647
PMID: 29315404
DOI: 10.1093/nar/gkx1312

[…] (1 mg/ml) for up to 14 days. subsequently, cells were fixed and stained with 20% ethanol-containing crystal violet solution (sigma-aldrich). colonies were counted manually or digitally using the opencfu software () with customized micros., for dual luciferase-mediated retrotransposition assays, hela cells (5  ×  104 cells/ml) were transfected using lipofectamine™ 3000 following […]


Insulin like growth factor receptor and sphingosine kinase are prognostic and therapeutic targets in breast cancer

PMCID: 5718000
PMID: 29207959
DOI: 10.1186/s12885-017-3809-0

[…] the cells were left to air-dry overnight and images obtained using fujifilm luminescent image analyzer las-300 and single colonies were counted using open colony forming unit (cfu) software (, 3 × 105 mcf7 and hcc-1806 breast cancer cell-lines were plated per well of 6-well plates, cultured for 24 h and subsequently treated with osi-906 (0.1, 0.4 or 1.6 μm) […]


Construction of a system using a deep learning algorithm to count cell numbers in nanoliter wells for viable single cell experiments

PMCID: 5715092
PMID: 29203784
DOI: 10.1038/s41598-017-17012-x

[…] of samples., automated methods for characterizing cells using microscopic images have been developed, requiring the use of software such as cellprofiler, imagej, imagej macro cell colony edge, and opencfu. in these methods, the images are treated by developer-defined procedures. methods using machine learning to characterize cells in microscopic images have also been reported. for example, […]


In vitro characterization of CD133lo cancer stem cells in Retinoblastoma Y79 cell line

PMCID: 5698942
PMID: 29162051
DOI: 10.1186/s12885-017-3750-2

[…] the resulting colonies were then fixed with 3.7% paraformaldehyde and stained with crystal violet. the images of the colonies were taken at 1.5x and 4x magnification and analysed using imagej and opencfu software. for colony forming efficiency (cfe) analysis, colonies greater than 50 cells were counted and percentage of colonies were calculated. the morphology of the colonies was assessed […]

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OpenCFU institution(s)
Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK; Institute for Biology, Free University of Berlin, Berlin, Germany
OpenCFU funding source(s)
This study is funded by the European Research Council.

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