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Citing

This page describes how to cite ImageJ and related projects.

  • For information on who contributes to these projects, see Contributors.
  • For information on who maintains these projects, see Governance.
  • For information on how these projects are funded, see Funding.

Guidelines

We ask users to cite:

  1. Any specific publications of plugins used.

  2. The general paper of ImageJ flavor(s) used; e.g.:

If journal reference limits interfere, the plugin-specific publications should take precedence.

In general, please cite these projects—their long-term future depends on it!

Thank you for your support.

ImageJ and variants

Supporting libraries

SciJava
SciJava Common
Rueden, C., Schindelin, J., Hiner, M. & Eliceiri, K. (2021). SciJava Common [Software]. https://scijava.org/.
ImageJ2
ImageJ Ops
Rueden, C., Dietz, C., Horn, M., Schindelin, J., Northan, B., Berthold, M. & Eliceiri, K. (2021). ImageJ Ops [Software]. https://imagej.net/Ops.

Citable software

The following table lists all citable software packages, plugins, etc., documented on the site. To add a tool to this list, add the doi: for its publication to the tool’s wiki page.

Project Publication(s) to cite
Bio-Formats doi:10.1083/jcb.201004104
Flavors of ImageJ doi:10.1002/mrd.22489
IJ-OpenCV doi:10.1016/j.compbiomed.2017.03.027
ImageJ Ops Rueden, C., Dietz, C., Horn, M., Schindelin, J., Northan, B., Berthold, M. & Eliceiri, K. (2021). ImageJ Ops [Software]. https://imagej.net/Ops.
ImgLib2 doi:10.1093/bioinformatics/bts543
SCIFIO doi:10.1186/s12859-016-1383-0
SciJava Rueden, C., Schindelin, J., Hiner, M. & Eliceiri, K. (2021). SciJava Common [Software]. https://scijava.org/.
TensorFlow doi:10.5281/zenodo.4724125
Guillaume Jacquemet doi:10.1083/jcb.201704045
3D ImageJ Suite doi:10.1093/bioinformatics/btt276
3D Viewer doi:10.1186/1471-2105-11-274
3Dscript doi:10.1038/s41592-019-0359-1
AccPbFRET doi:10.1186/1471-2105-9-346
ActionBar doi:10.6084/m9.figshare.3397603
ActogramJ doi:10.1177/0748730411414264
AdipoQ doi:10.1091/mbc.E21-11-0592
ALPACA doi:10.1038/s41431-021-00907-9
AnalyzeSkeleton doi:10.1002/jemt.20829
Anisotropic Diffusion 2D doi:10.1109/TPAMI.2005.87
Atlas Toolkit doi:10.1038/srep20732
AxoNet doi:10.48550/arXiv.1908.02919
Balloon segmentation doi:10.1038/nmeth.1940
BAR doi:10.5281/zenodo.28838
BigDataViewer doi:10.1038/nmeth.3392
BigWarp doi:10.1109/ISBI.2016.7493463
Bleach Correction doi:10.12688/f1000research.27171.1
BoneJ doi:10.12688/wellcomeopenres.16619.2
BoneJ1 doi:10.1016/j.bone.2010.08.023
CiliaQ doi:10.1140/epje/s10189-021-00031-y
ClearVolume doi:10.1038/nmeth.3372
ColonyArea doi:10.1371/journal.pone.0092444
Distortion Correction doi:10.1016/j.jsb.2010.04.012
DS4H Image Alignment doi:10.3389/fimmu.2019.02353
Ellipse split doi:10.5281/zenodo.834339
Fast4DReg doi:10.1088/1361-6463/ab0261
FigureJ doi:10.1111/jmi.12069
Fiji Z-Spacing Correction doi:10.1109/ISBI.2015.7163922
FijiWings doi:10.1534/g3.113.006676
FiloQuant doi:10.1083/jcb.201704045
FLIMJ doi:10.1371/journal.pone.0238327
Frangi doi:10.1007/BFb0056195
FreQ doi:10.1016/j.xpro.2022.101542
Glasbey doi:10.1002/col.20327
Granulometric Filtering doi:10.1016/j.jneumeth.2005.07.011
IJ Blob doi:10.5334/jors.ae
Image Stitching doi:10.1093/bioinformatics/btp184
IsletJ doi:10.3727/096368916X692005
Iterative Deconvolve 3D doi:10.2514/6.2005-2961
JaCoP doi:10.1111/j.1365-2818.2006.01706.x
Labkit - Intuitive Pixel Classification in Fiji doi:10.3389/fcomp.2022.777728
LimeSeg doi:10.1186/s12859-018-2471-0
Linear Stack Alignment with SIFT doi:10.1023/B:VISI.0000029664.99615.94
Low Light Tracking Tool doi:10.1364/OE.22.000210
LungJ doi:10.5258/SOTON/401280
Getting started with MaMuT doi:10.7554/eLife.34410
MaMuT doi:10.7554/eLife.34410
Microscope Focus Quality doi:10.1186/s12859-018-2087-4
MiToBo doi:10.5334/jors.103
ModularImageAnalysis (MIA) doi:10.5281/zenodo.1201320
MorphoLibJ doi:10.1093/bioinformatics/btw413
MotiQ doi:10.1091/mbc.E21-11-0585
Moving Least Squares doi:10.1145/1179352.1141920
MTrack doi:10.1038/s41598-018-37767-1
Multifrac doi:10.1016/j.softx.2020.100574
NeuronDetector doi:10.5281/zenodo.1400718
Non Local Means Denoise
Pendent Drop doi:10.5334/jors.97
PhotoBend doi:10.1039/C7SC04863G
PixFRET doi:10.1002/jemt.20215
QuickFigures doi:10.1371/journal.pone.0240280
QuickPALM doi:10.1038/nmeth0510-339
RETINA Analysis Toolkit doi:10.1167/iovs.15-17599
Ridge Detection doi:10.5281/zenodo.845874
RiFRET
SampEn2D
Shape Filter doi:10.5334/jors.ae
SNT › Sholl Analysis doi:10.1038/nmeth.3125
Sigma Filter doi:10.1016/0734-189X(83)90047-6
Skeletonize3D doi:10.1002/jemt.20829
SME Projection doi:10.1038/ncomms15554
SNT doi:10.1038/s41592-021-01105-7
SNT › Machine Learning
SNT › Modeling
SpermQ doi:10.3390/cells8010010
Spot Spine doi:10.12688/f1000research.146327.1
Sprout Morphology doi:10.1186/s41232-016-0033-2
StarDist doi:10.1007/978-3-030-00934-2_30
Statistical Region Merging doi:10.1109/TPAMI.2004.110
StereoMate doi:10.1101/648337
Stitching 2D/3D doi:10.1093/bioinformatics/btp184
Stochastic Denoise doi:10.5244/C.23.117
SNT › Strahler Analysis (From Images) doi:10.1038/s41592-021-01105-7
TrackMate Actions doi:10.1101/2021.09.03.458852
TrackMate-ExTrack doi:10.1083/jcb.202208059
TrackMate DoG detector doi:10.1101/2021.09.03.458852
Extending TrackMate doi:10.1101/2021.09.03.458852
TrackMate doi:10.1101/2021.09.03.458852
Using TrackMate from MATLAB doi:10.1101/2021.09.03.458852
TrackMate Accuracy doi:10.1101/2021.09.03.458852
Manual editing of tracks using TrackMate doi:10.1101/2021.09.03.458852
Manual tracking with TrackMate doi:10.1101/2021.09.03.458852
Shortcuts for editing and navigating the main view of TrackMate doi:10.1101/2021.09.03.458852
TrakEM2 doi:10.1371/journal.pone.0038011
Tubeness doi:10.1016/s1361-8415(98)80009-1
Trainable Weka Segmentation doi:10.1093/bioinformatics/btx180
Large-scale cell tracking under segmentation uncertainty doi:10.48550/arXiv.2308.04526
VTEA › Volumetric Tissue Exploration and Analysis doi:10.1681/ASN.2016091027
Zellige doi:10.1101/2022.04.05.485876
MATLAB Scripting doi:10.1093/bioinformatics/btw681
PyImageJ doi:10.1038/s41592-022-01655-4
Alida doi:10.5334/jors.124
Bio7 doi:10.18637/jss.v049.i04
BioImageXD doi:10.1038/nmeth.2047
CellProfiler
Endrov doi:10.1038/nmeth.2478
Fiji doi:10.1038/nmeth.2019
FunImageJ doi:10.1093/bioinformatics/btx710
Icy doi:10.1038/nmeth.2075
ImageJ doi:10.1038/nmeth.2089
ImageJ2 doi:10.1186/s12859-017-1934-z
ImagePy doi:10.1093/bioinformatics/bty313
ImJoy doi:10.1038/s41592-019-0627-0
ITK doi:10.3233/978-1-60750-929-5-586
KNIME Analytics Platform
MBF Plugin Collection doi:10.2144/000112517
Micro-Manager doi:10.1002/0471142727.mb1420s92
napari doi:10.5281/zenodo.3555620
NIH Image doi:10.1038/nmeth.2089
OMERO
OpenSPIM doi:10.1038/nmeth.2507
QuPath doi:10.1038/s41598-017-17204-5
Virtual Cell doi:10.1016/S0167-7799(01)01740-1
VisBio doi:10.1111/j.1600-0854.2004.00189.x

See also