ImageJ protocols

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ImageJ specifications


Unique identifier OMICS_13947
Name ImageJ
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 2.0.0
Stability Stable
Maintained Yes



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  • person_outline Kevin Eliceiri <>
  • person_outline Curtis Rueden <>
  • person_outline Wayne Rasband <>
  • person_outline Jeff Hardin <>

Additional information; (Rueden et al., 2017) ImageJ2: ImageJ for the next generation of scientific image data. 2017.arXiv.

Publications for ImageJ

ImageJ in pipelines

PMCID: 5778106
PMID: 29403481
DOI: 10.3389/fimmu.2017.02001

[…] (santa cruz biotechnology). nuclei were labeled using dapi (sigma). images were acquired using a zeiss lsm 780 confocal microscope and analyzed using imaris (bitplane), volocity (perkin elmer), and imagej (nih). one to four slices were randomly selected from at least three animals per group. for quantification of infiltrated islets, four slices were randomly selected from pancreas from at least […]

PMCID: 5356445
PMID: 28148823
DOI: 10.1098/rsob.160312

[…] in ms-222 (sigma) and kept at 28.5°c. we used sp5 (leica), lsm 880 (zeiss), lsm 710 (zeiss) laser scanning or spinning disk (perkinelmer) confocal microscopes. for image data analysis, we used imagej (, volocity (perkinelmer) or imaris (bitplane) software., all statistical analyses were performed using prism7 (graphpad software). to compare the differences […]

PMCID: 5425629
PMID: 28416284
DOI: 10.1016/j.stemcr.2017.03.016

[…] (42–54 hpf), runx1+144:gfp+/flk1:dsred+ embryos were embedded in 0.8%–2% low-melting agarose with tricaine (sigma) and mounted on 35-mm center-glass dishes. image analysis was performed using imagej (nih), volocity (perkinelmer), or imaris (bitplane) software., runx1+144:gfp+ embryos were incubated at 72 hpf on ice for 10 min, followed by a 2-hr incubation in 400 μm edu (4% dmso/e3 […]

PMCID: 5540285
PMID: 28767724
DOI: 10.1371/journal.pone.0181579

[…] were made using volocity software (perkin elmer) and imaris scientific 3d/4d image processing analysis software (bitplane ag, zurich, switzerland). images analyses were performed using imagej software and lsm image analyzer software from zeiss. invadopodia degraded areas were measured with imagej software by a manual threshold cut off of non fluorescent areas to allow the binary […]

PMCID: 5547041
PMID: 28785031
DOI: 10.1038/s41598-017-07614-w

[…] carlsbad, california) using the omx editor software. reconstructed images were analysed in volocity and imaris software, while prelamin a brightness at different nuclear loci was quantified in imagej., initially, lamin b1 cdna was cloned into mkikgr-c1 (a gift from michael davidson; addgene plasmid # 54656) between bglii and xmai restriction sites. then region encoding mkikgr tag […]

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ImageJ in publications

PMCID: 5953022
PMID: 29739136
DOI: 10.9758/cpn.2018.16.2.214

[…] with a peroxidase-conjugated secondary antibody (1:2,500) for 2 hours at room temperature. specific bands were detected using the ecl system and were analyzed using image j software ( for quantification purposes. β-actin was used as a loading control and the immunoblotting intensity was normalized withβ-actin immunoreactivity., ibm spss statistics ver. […]

PMCID: 5964350
DOI: 10.1128/mBio.02325-17

[…] (1:200), and coverslips were mounted in prolong gold anti-fade reagent (invitrogen) and examined on a leica sp5 confocal microscope (leica microsystems, inc.). image analysis was performed using imagej () and the jacop plug-in (). three areas per image of 120 by 120 pixels with high accumulation of 3a protein were analyzed to determine pearson’s coefficient (pc). pc values below 0.6 […]

PMCID: 5964347
DOI: 10.1128/mBio.00738-18

[…] yde for 1 h at room temperature, mounted in prolong gold, and stained with 4′,6-diamidino-2-phenylindole (dapi). virus absorption was measured based on the mean bodipy fluorescence per cell and using imagej., an alexafluor 568-conjugated probe was adhered to the 5′ end of the partial zikv 5′-utr sequence: 5′-ctactccgcgttttagcatattgacaatccggaatcctccgg-3′. w+ and w− cells were plated at 3.5 × 105 ce […]

PMCID: 5959882
PMID: 29777131
DOI: 10.1038/s41467-018-04472-6

[…] dotted onto whattman paper and exposed to a photostimulable phosphor (psp) plate overnight. amounts of incorporated radioactivity were then visualized using a phosphorimager and quantified with imagej., salmonella tact2seny137f and tact2stmy137f sequences encoding the residues were expressed as a n-terminal (his)7 fusion protein of the pqlinkh::tact2y137f vector. e. coli, strain pc2, […]

PMCID: 5959871
PMID: 29777103
DOI: 10.1038/s41467-018-04227-3

[…] added to protein solutions in 1× cutsmart buffer (new england biolabs) and incubated for 1 h at 37 °c. for densitometric determination of sds-page bands, band intensity integrals were measured using imagej (nih)., for detection of native encapsulin nanocompartments, the nativepage™ novex® bis-tris gel system (life technologies) was used. either eluted material from the co-ip/purification […]

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ImageJ institution(s)
Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA
ImageJ funding source(s)
Supported by the National Institute of General Medical Sciences (NIGMS) through the American Recovery and Reinvestment Act of 2009 NIH Research and Research Infrastructure “Grand Opportunities” Grant, “Hardening” of Biomedical Informatics/Computing Software for Robustness and Dissemination (Ref: RC2 GM092519-01), as well as a Wellcome Trust Strategic Award (Ref: 095931); by the National Science Foundation, award number 1148362; by the Laboratory for Optical and Computational Instrumentation, and the Morgridge Institute for Research.

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