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FindFoci specifications


Unique identifier OMICS_25483
Name FindFoci
Software type Package/Module, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available



  • person_outline Alex Herbert <>

Publication for FindFoci

FindFoci citations


Phosphorylation of Serine 225 in Hepatitis C Virus NS5A Regulates Protein Protein Interactions

PMCID: 5553161
PMID: 28615203
DOI: 10.1128/JVI.00805-17

[…] of ns5a spatial arrangement, images were acquired with the same acquisition parameters, but with variable gain to ensure correct exposure. the spatial coordinates of ns5a were determined using the findfoci function of the gdsc plugin for fiji, with the nuclear envelope being manually outlined (utilizing the dapi staining as a reference) and coordinates generated by fiji. the distance […]


Ultrastructural and Functional Properties of a Giant Synapse Driving the Piriform Cortex to Mediodorsal Thalamus Projection

PMCID: 5281591
PMID: 28197093
DOI: 10.3389/fnsyn.2017.00003

[…] the soma and the synapse. the plug-in searches for the brightest trace (and its length) of voxels in 3d between manually selected spots., all images were processed with fiji and additional plug-ins: findfoci (herbert et al., ) and 3d roi manager (ollion et al., ). the findfoci plug-in was used to find the volume of the synapse. the search parameters were set to auto threshold (mean + 3x sd). […]


Unique geometry of sister kinetochores in human oocytes during meiosis I may explain maternal age associated increases in chromosomal abnormalities

PMCID: 4823989
PMID: 26718930
DOI: 10.1242/bio.016394

[…] if foci could not be reliably classified, for instance due to overlapping chromosomes or kinetochore signal, they were classified as unclear. inter-kinetochore distance was measured using the findfoci plugin in imagej, which identifies regions of peak intensity in 3d image stacks (). for kinetochores in different z-sections, the pythagorean formula was used to calculate inter-kinetochore […]


The Focinator a new open source tool for high throughput foci evaluation of DNA damage

PMCID: 4554354
PMID: 26238507
DOI: 10.1186/s13014-015-0453-1

[…] the source code for an imagej macro without interface, like a menu and buttons [], and du and colleagues developed a tool for foci picking without batch mode and automated foci selection []. the findfoci plugin for imagej supports self-learning parameters but does not support multi-channel analysis []. thus, there was a demand for the development of easy-to-use, customizable and reliable […]


Serine Phosphorylation of the Hepatitis C Virus NS5A Protein Controls the Establishment of Replication Complexes

PMCID: 4337517
PMID: 25552726
DOI: 10.1128/JVI.02995-14

[…] were acquired by use of the same acquisition parameters described above, but a variable gain was used to ensure the correct exposure. the spatial coordinates of the lds were determined using the findfoci function of the gdsc plug-in for fiji software, with the nuclear envelope being manually outlined (utilizing dapi [4′,6-diamidino-2-phenylindole] staining as a reference), […]

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FindFoci institution(s)
MRC Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
FindFoci funding source(s)
Supported by Medical Research Council grant G1100074 and by a Senior Research Nonclinical Fellowship G0902043 from the Medical Research Council, UK.

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