Page history Edit this page How do I edit this website?

Citing

This page describes how to cite SciJava projects.

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

Guidelines

We ask users to cite:

  1. Any specific publications of plugins used.
  2. The general paper of ImageJ distribution(s) used—e.g., if you used Fiji, cite the Fiji paper.
  3. The general ImageJ paper.

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.

Core projects

Distributions of ImageJ

Supporting libraries

SciJava
SciJava Common
Rueden, C., Schindelin, J., Hiner, M. & Eliceiri, K. (2021). SciJava Common [Software]. https://scijava.org/.
ImageJ
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
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
Sigma Filter doi:10.1016/0734-189X(83)90047-6
Skeletonize3D doi:10.1002/jemt.20829
SME Projection doi:10.1038/ncomms15554
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:10.1002/mrd.22489
ImageJ1 doi:10.1038/nmeth.2089
ImageJ2 doi:10.1186/s12859-017-1934-z
ImagePy doi:10.1093/bioinformatics/bty313
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