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Fiji specifications


Unique identifier OMICS_18877
Name Fiji
Alternative name Fiji Is Just ImageJ
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Programming languages Python, Ruby, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Medium
Version 2.0.0
Stability Stable
Maintained Yes




No version available



  • person_outline Pavel Tomančák
  • person_outline Albert Cardona

Additional information

Publication for Fiji Is Just ImageJ

Fiji citations


Concepts in Light Microscopy of Viruses

PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] l hundred analysis plugins. A deep strength of ImageJ is the ease with which additional plugins can be generated, modified, and installed. The prime example for this is Fiji, a recursive acronym for “Fiji Is Just ImageJ”. Fiji is an implementation of ImageJ which is expanded by many plugins, as well as an integrated updating system and developer tools []. Several plugins perform surprisingly compl […]


Supramolecular assembly of the beta catenin destruction complex and the effect of Wnt signaling on its localization, molecular size, and activity in vivo

PLoS Genet
PMCID: 5912785
PMID: 29641560
DOI: 10.1371/journal.pgen.1007339

[…] Stage 9 embryos were stained with antibody to Engrailed and imaged on a Zeiss LSM 710 or 880 scanning confocal microscope. Images were processed using FIJI (Fiji Is Just ImageJ) as follows: maximum intensity projections 8μm thick were created and thresholded to highlight cells expressing Engrailed and eliminate background noise. Three lines parallel to th […]


The epicardium obscures interpretations on endothelial to mesenchymal transition in the mouse atrioventricular canal explant assay

Sci Rep
PMCID: 5856756
PMID: 29549339
DOI: 10.1038/s41598-018-22971-w
call_split See protocol

[…] FIJI (Fiji is just ImageJ), GIMP (GNU image manipulation program) and Inkscape were used for image processing. […]


Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases mediate membrane fusion at the vacuole in Arabidopsis

Proc Natl Acad Sci U S A
PMCID: 5877921
PMID: 29463724
DOI: 10.1073/pnas.1717839115

[…] ar membrane labeled by YFP-VAMP711 was determined and their ratio calculated. Statistical analysis was performed with OriginPro 2017 (OriginLabs). Image postprocessing operations were done with Fiji (Fiji Is Just ImageJ, based on ImageJ 1.51d;; ref. ). […]


Fractal analysis of plaque border, a novel method for the quantification of atherosclerotic plaque contour irregularity, is associated with pro atherogenic plasma lipid profile in subjects with non obstructive carotid stenoses

PLoS One
PMCID: 5809053
PMID: 29432486
DOI: 10.1371/journal.pone.0192600

[…] Fractal analysis was performed on long axis views of carotid artery plaques using the open source image processing software Fiji (Fiji Is Just ImageJ,[] First, the images were thresholded and binarized using an automated thresholding technique, a modified variation of the IsoData algorithm, default thresholdin […]


The bacterial pigment pyocyanin inhibits the NLRP3 inflammasome through intracellular reactive oxygen and nitrogen species

PMCID: 5880120
PMID: 29414783
DOI: 10.1074/jbc.RA117.001105

[…] 88 nm) and subtracted autofluorescence in response to 405-nm excitation. At the end of each experiment, we added 2 mm DTT and 16 mm H2O2 to fully reduce/oxidize the probe. We analyzed the images with Fiji Is Just ImageJ (Fiji) and excluded detached cells from the analysis. Ratios were normalized to percent oxidation as described previously (). […]


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Fiji institution(s)
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Berkeley Drosophila Genome Project, Department of Genome Dynamics, Lawrence Berkeley National Labs, Berkeley, CA, USA; Department of Computer Science, of the Swiss Federal Institute of Technology Zürich, Switzerland; Institute of Neuroinformatics of the University of Zürich and Swiss Federal Institute of Technology Zürich, Switzerland; University of Wisconsin at Madison, LOCI, Madison, WI, USA; University of Würzburg, Department of Neurobiology and Genetics, Würzburg, Germany; Institute Pasteur, La plate-forme d’imagerie dynamique - imagopole, Paris, France; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
Fiji funding source(s)
Supported by Human Frontier Science Program Young Investigator Grant RGY0083; The European Research Council Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 260746.

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