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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 Viewer doi:10.1186/1471-2105-11-274
3Dscript doi:10.1038/s41592-019-0359-1
AccPbFRET doi:10.1186/1471-2105-9-346
ActogramJ doi:10.1177/0748730411414264
AnalyzeSkeleton doi:10.1002/jemt.20829
Anisotropic Diffusion 2D doi:10.1109/TPAMI.2005.87
Atlas Toolkit doi:10.1038/srep20732
Balloon doi:10.1038/nmeth.1940
BAR doi:10.5281/zenodo.28838
BigDataViewer doi:10.1038/nmeth.3392
BigWarp doi:10.1109/ISBI.2016.7493463
BoneJ doi:10.12688/wellcomeopenres.16619.2
BoneJ1 doi:10.1016/j.bone.2010.08.023
ClearVolume doi:10.1038/nmeth.3372
Distortion Correction doi:10.1016/j.jsb.2010.04.012
Ellipse split doi:10.5281/zenodo.834339
FigureJ doi:10.1111/jmi.12069
FijiWings doi:10.1534/g3.113.006676
FiloQuant doi:10.1083/jcb.201704045
Frangi doi:10.1007/BFb0056195
Glasbey doi:10.1002/col.20327
Granulometric Filtering doi:10.1016/j.jneumeth.2005.07.011
IJ Blob doi:10.5334/jors.ae
IsletJ doi:10.3727/096368916X692005
Iterative Deconvolve 3D doi:10.2514/6.2005-2961
JaCoP doi:10.1111/j.1365-2818.2006.01706.x
Linear Stack Alignment with SIFT doi:10.1023/B:VISI.0000029664.99615.94
LungJ doi:10.5258/SOTON/401280
MaMuT doi:10.7554/eLife.34410
Microscope Focus Quality doi:10.1186/s12859-018-2087-4
MiToBo doi:10.5334/jors.103
MorphoLibJ doi:10.1093/bioinformatics/btw413
Moving Least Squares doi:10.1145/1179352.1141920
Multifrac doi:10.1016/j.softx.2020.100574
NeuronDetector doi:10.5281/zenodo.1400718
Pendent Drop doi:10.5334/jors.97
PhotoBend doi:10.1039/C7SC04863G
PixFRET doi:10.1002/jemt.20215
QuickPALM doi:10.1038/nmeth0510-339
RETINA Analysis Toolkit doi:10.1167/iovs.15-17599
RiFRET doi:10.1002/cyto.a.20747
SampEn2D
Sholl Analysis doi:10.1038/nmeth.3125
Sigma Filter doi:10.1016/0734-189X(83)90047-6
Simple Neurite Tracer doi:10.1093/bioinformatics/btr390
Skeletonize3D doi:10.1002/jemt.20829
SME Projection doi:10.1038/ncomms15554
SNT doi:10.1038/s41592-021-01105-7
SNT › Modeling doi:10.3389/neuro.10.025.2009
SNT › Tubular Geodesics doi:10.1109/cvpr.2012.6247722
Sprout Morphology doi:10.1186/s41232-016-0033-2
Statistical Region Merging doi:10.1109/TPAMI.2004.110
StereoMate doi:10.1101/648337
Strahler Analysis doi:10.5281/zenodo.49399
TrackMate doi:10.1016/j.ymeth.2016.09.016
TrakEM2 doi:10.1371/journal.pone.0038011
Trainable Weka Segmentation doi:10.1093/bioinformatics/btx180
VTEA › Volumetric Tissue Exploration and Analysis doi:10.1681/ASN.2016091027
MATLAB Scripting doi:10.1093/bioinformatics/btw681
Alida doi:10.5334/jors.124
Bio7 doi:10.18637/jss.v049.i04
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
Micro-Manager doi:10.1002/0471142727.mb1420s92
NIH Image doi:10.1038/nmeth.2089
OMERO
OpenSPIM doi:10.1038/nmeth.2507
Virtual Cell doi:10.1016/S0167-7799(01)01740-1

See also