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This page lists publications relating to the Fiji project.

Publications introducing Fiji

  • A paper about the ImageJ software ecosystem—including ImageJ itself, ImageJ2, Fiji, related SciJava projects, and various plugins—was published in Molecular Reproduction and Development in July 20152.
  • Fiji was prominently featured in Nature Methods review supplement on visualization 4
  • A review of biological imaging software tools focusses on open source programs and Fiji is a big part of it5.
  • A German article about Fiji was published in the popular scientific journal Laborwelt (with one erratum: the authors would never claim that Fiji succeeds ImageJ; rather, Fiji Is Just ImageJ).

Publications using or enhancing Fiji

  • Fiji’s 3D Viewer was published in BMC Bioinformatics8
  • A powerful plugin for registering SPIM (Selective Plane Illumination Microscopy) and other multi-angle image data was published in Nature Methods9
  • TrakEM2 was used and enhanced to identify neuronal lineages, and an article was published in the Journal of Neuroscience10 about it.
  • The algorithms behind TrakEM2 registration were presented at the ISMB conference and published in Bioinformatics.11
  • TrakEM2 finally got its well deserved primary reference through the PLoS Biology paper on neuronal architecture of the fruitfly brain.13
  • Not so simple Simple_Neurite_Tracer, a product of the hard work of Mark Longair and one of the premier Fiji projects was published in Bioinformatics. 15
  • We wanted to have the Balloon segmentation plugin in Fiji for a long time and our request for the source code pushed the corresponding Nature Methods paper16 forward. Thanks Lionel Dupuy!
  • A commentary by Albert Cardona and Pavel Tomancak discusses the impact and problems open source software development faces in academia18.
  • Albert Cardona’s TrakEM2 was published in PLoS One19.
  • ImgLib2 was published in Bioinformatics. The library developed jointly by Stephan Saalfeld, Stephan Preibisch and Tobias Pietzsch has originated in Fiji but has outgrown it becoming the centerpiece of other projects, especially ImageJ2 Pavel Tomancak provided funding for its developers.20.
  • OpenSPIM21 relies heavily on Fiji for microscope operation and SPIMage processing.
  • The 2D and 3D Particle Tracker algorithm available in Fiji though the MOSAICsuite plugin performed well in a recent comparative study of many particle tracking tools: Chenouard et al. (201424).
  • The globally optimal Squassh segmentation algorithm available in the MOSAICsuite plugin includes cutting-edge developments from computer vision as described in Paul, Cardinale, and Sbalzarini (201325). It optionally also corrects for the microscope PSF, providing deconvolving segmentation as described in Helmuth et al. (200926) and in Helmuth and Sbalzarini (200927)
  • The Squassh workflow for segmentation and quantification of subcellular shapes in fluorescence microscopy images has been published in in Rizk et al. (201428).
  • The Region Competition algorithm has been published in Cardinale, Paul, and Sbalzarini and Koumoutsakos (201229). It provides a flexible and powerful tool for segmenting fluorescence-microscopy images. It can handle arbitrary numbers of objects that can additionally be shaded. It optionally also corrects for the microscope PSF, providing deconvolving segmentation as described in Helmuth et al. (200930) and in Helmuth and Sbalzarini (200931).
  • Interaction analysis as provided by the MosaicIA plugin extends the concept of colocalization analysis to spatial patterns and allows directly estimating interactions between imaged objects from the image, as described in Helmuth, Paul, and Sbalzarini (201032).
  • TrackMate was published 6 years after the initial commit, in a special edition of the Methods35 journal dedicated to open source software for Life Sciences.


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  1. Invalid citation arguments: {"fn"=>1, "content"=>"journal", "author"=>"Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak and Albert Cardona", "title"=>"Fiji: an open-source platform for biological-image analysis", "journal"=>"Nature Methods", "year"=>"2012", "volume"=>"9(7)", "pages"=>"676-682", "url"=>""}

  2. doi:10.1002/mrd.22489 

  3. Invalid citation arguments: {"fn"=>3, "content"=>"conference", "author"=>"Schindelin J", "title"=>"Fiji Is Just ImageJ (batteries included)", "year"=>"2008", "month"=>"November"}

  4. Invalid citation arguments: {"fn"=>4, "content"=>"journal", "author"=>"Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider, Pavel Tomancak and Jean-Karim Hériché", "title"=>"Visualization of image data from cells to organisms", "journal"=>"Nature Methods", "year"=>"2010", "volume"=>"7 No 3s", "pages"=>"S26 -S41", "url"=>""}

  5. Invalid citation arguments: {"fn"=>5, "content"=>"journal", "author"=>"Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibàñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak & Anne E Carpenter", "title"=>"Biological imaging software tools", "journal"=>"Nature Methods", "year"=>"2012", "volume"=>"9(7)", "pages"=>"697–710", "url"=>""}

  6. Invalid citation arguments: {"fn"=>6, "content"=>"journal", "author"=>"Preibisch S and Saalfeld S and Tomancak P", "title"=>"Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions", "journal"=>"Bioinformatics", "year"=>"2009", "month"=>"April", "volume"=>"25(11)", "pages"=>"1463-1465", "pmid"=>"19346324", "url"=>""}

  7. Invalid citation arguments: {"fn"=>7, "content"=>"journal", "author"=>"Hegge S and Kudryashev M and Smith A and Frischknecht F", "title"=>"Automated classification of <I>Plasmodium</I> sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection", "journal"=>"Biotechnology Journal", "year"=>"2009", "month"=>"May", "pmid"=>"19455538", "url"=>""}

  8. Invalid citation arguments: {"fn"=>8, "content"=>"journal", "author"=>"Benjamin Schmid , Johannes Schindelin , Albert Cardona , Mark Longair and Martin Heisenberg", "title"=>"A high-level 3D visualization API for Java and ImageJ", "journal"=>"BMC Bioinformatics", "year"=>"2010", "volume"=>"11", "pages"=>"274", "url"=>""}

  9. Invalid citation arguments: {"fn"=>9, "content"=>"journal", "author"=>"Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin and Pavel Tomancak", "year"=>"2010", "title"=>"Software for bead-based registration of selective plane illumination microscopy data", "journal"=>"Nature Methods", "volume"=>"7", "pages"=>"418-419", "url"=>""}

  10. doi:10.1523/JNEUROSCI.0186-10.2010 

  11. doi:10.1093/bioinformatics/btq219 

  12. doi:10.1016/j.jsb.2010.04.012 

  13. doi:10.1371/journal.pbio.1000502 

  14. Invalid citation arguments: {"fn"=>14, "content"=>"journal", "author"=>"Verena Kaynig, Thomas Fuchs, Joachim M. Buhmann", "title"=>"Neuron Geometry Extraction by Perceptual Grouping in ssTEM Images", "journal"=>"CVPR", "year"=>"2010", "url"=>""}

  15. Invalid citation arguments: {"fn"=>15, "content"=>"journal", "author"=>"Longair Mark, Baker DA, Armstrong JD.", "title"=>"Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes.", "journal"=>"Bioinformatics", "year"=>"2011", "url"=>""}

  16. Invalid citation arguments: {"fn"=>16, "content"=>"journal", "author"=>"Federici Fernán, Dupuy Lionel, Laplaze Laurent, Heisler Marcus, Haseloff Jim.", "title"=>"Integrated genetic and computation methods for in planta cytometry", "journal"=>"Nature Methods", "year"=>"2012", "volume"=>"advance online publication", "url"=>""}

  17. doi:10.1038/nmeth.2072 

  18. Invalid citation arguments: {"fn"=>18, "content"=>"journal", "author"=>"Albert Cardona and Pavel Tomancak", "title"=>"Current challenges in open-source bioimage informatics", "journal"=>"Nature Methods", "year"=>"2012", "volume"=>"9(7)", "pages"=>"661–665", "url"=>""}

  19. doi:10.1371/journal.pone.0038011 

  20. Invalid citation arguments: {"fn"=>20, "content"=>"journal", "author"=>"Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld", "title"=>"ImgLib2 – Generic Image Processing in Java", "journal"=>"Bioinformatics", "year"=>"2012", "volume"=>"28(22)", "pages"=>"3009-3011", "url"=>""}

  21. Invalid citation arguments: {"fn"=>21, "content"=>"journal", "author"=>"Pitrone P. G., Schindelin J., Stuyvenberg L., Preibisch S., Weber M.; Eliceiri K. W., Huisken J., Tomancak P.", "title"=>"OpenSPIM: an open access light sheet microscopy platform", "journal"=>"Nature Methods", "volume"=>"", "number"=>"", "pages"=>"", "year"=>"2013", "url"=>""}

  22. Invalid citation arguments: {"fn"=>22, "content"=>"journal", "author"=>"Krull, A., Steinborn A., Ananthanarayanan V., Ramunno-Johnson D., Petersohn U., Tolic-Norrelykke I. M.", "title"=>"A divide and conquer strategy for the maximum likelihood localization of low intensity objects.", "journal"=>"Optics Express", "volume"=>"22", "number"=>"1", "pages"=>"210-228", "year"=>"2014", "url"=>""}

  23. doi:10.1016/j.jsb.2005.06.002 

  24. doi:10.1038/nMeth.2808 

  25. doi:10.1007/s11263-013-0615-2 

  26. doi:10.1016/j.jsb.2009.03.017 

  27. J. A. Helmuth and I. F. Sbalzarini. Deconvolving active contours for fluorescence microscopy images, In Proc. Intl. Symp. Visual Computing (ISVC), volume 5875 of Lecture Notes in Computer Science, pages 544–553, Las Vegas, USA, November 2009. Springer. 

  28. doi:10.1038/nprot.2014.037 

  29. doi:10.1109/TIP.2012.2192129 

  30. doi:10.1016/j.jsb.2009.03.017 

  31. J. A. Helmuth and I. F. Sbalzarini. Deconvolving active contours for fluorescence microscopy images, In Proc. Intl. Symp. Visual Computing (ISVC), volume 5875 of Lecture Notes in Computer Science, pages 544–553, Las Vegas, USA, November 2009. Springer. 

  32. doi:10.1186/1471-2105-14-349 

  33. doi:10.1186/1471-2105-11-372 

  34. Ferreira T, Blackman A, Oyrer J, Jayabal A, Chung A, Watt A, Sjöström J, van Meyel D. Neuronal morphometry directly from bitmap images, Nature Methods 11(10): 982–984, 2014 

  35. Jean-Yves Tinevez, Nick Perry, Johannes Schindelin, Genevieve M. Hoopes, Gregory D. Reynolds, Emmanuel Laplantine, Sebastian Y. Bednarek, Spencer L. Shorte, Kevin W. Eliceiri, TrackMate: An open and extensible platform for single-particle tracking, Methods, Available online 3 October 2016, ISSN 1046-2023.