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Publications introducing Fiji

  • Fiji was prominently featured in Nature Methods review supplement on visualization [3]
  • A review of biological imaging software tools focusses on open source programs and Fiji is a big part of it[4].
  • 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

  • A powerful plugin for registering SPIM (Selective Plane Illumination Microscopy) and other multi-angle image data was published in Nature Methods[8]
  • TrakEM2 was used and enhanced to identify neuronal lineages, and an article was published in the Journal of Neuroscience[9] about it.
  • The algorithms behind TrakEM2 registration were presented at the ISMB conference and published in Bioinformatics.[10]
  • TrakEM2 finally got its well deserved primary reference through the PLoS Biology paper on neuronal architecture of the fruitfly brain.[12]
  • 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. [14]
  • 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 paper[15] forward. Thanks Lionel Dupuy!
  • A commentary by Albert Cardona and Pavel Tomancak discusses the impact and problems open source software development faces in academia[17].
  • Albert Cardona's TrakEM2 was published in PLoS One[18].
  • 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.[19].
  • OpenSPIM[20] relies heavily on Fiji for microscope operation and SPIMage processing.
  • MosaicSuite[21] from Ivo Sbalzarini's lab published in BMC Bioinformatics.


  1. 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 (2012), "Fiji: an open-source platform for biological-image analysis", Nature Methods 9(7): 676-682, <>
  2. Schindelin J (November 2008). "Fiji Is Just ImageJ (batteries included)".. 
  3. 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 (2010), "Visualization of image data from cells to organisms", Nature Methods 7 No 3s: S26 -S41, <>
  4. 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 (2012), "Biological imaging software tools", Nature Methods 9(7): 697–710, <>
  5. Preibisch S and Saalfeld S and Tomancak P (April 2009), "Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions", Bioinformatics 25(11): 1463-1465, PMID 19346324, <>
  6. Hegge S and Kudryashev M and Smith A and Frischknecht F (May 2009), "Automated classification of Plasmodium sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection", Biotechnology Journal, PMID 19455538, <>
  7. Benjamin Schmid , Johannes Schindelin , Albert Cardona , Mark Longair and Martin Heisenberg (2010), "A high-level 3D visualization API for Java and ImageJ", BMC Bioinformatics 11: 274, <>
  8. Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin and Pavel Tomancak (2010), "Software for bead-based registration of selective plane illumination microscopy data", Nature Methods 7: 418-419, <>
  9. Albert Cardona, Stephan Saalfeld, Ignacio Arganda, Wayne Pereanu, Johannes Schindelin and Volker Hartenstein (2010), "Identifying Neuronal Lineages of Drosophila by Sequence Analysis of Axon Tracts", The Journal of Neuroscience 30(22): 7538-7553, doi:10.1523/JNEUROSCI.0186-10.2010, <>
  10. Stephan Saalfeld, Albert Cardona, Volker Hartenstein and Pavel Tomancak (2010), "As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets", Bioinformatics 26(12): i57-63, doi:10.1093/bioinformatics/btq219, <>
  11. Verena Kaynig, Bernd Fischer, Elisabeth Müller, and Joachim M. Buhmann (2010), "Fully automatic stitching and distortion correction of transmission electron microscope images", Journal of Structural Biology 171(2): 163-173, doi:10.1016/j.jsb.2010.04.012, <>
  12. Cardona Albert, Saalfeld Stephan, Preibisch Stephan, Schmid Benjamin, Cheng Anchi, Pulokas Jim, Tomancak Pavel, Hartenstein Volker (2010), "An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy", PLoS Biology 8(10): e1000502, doi:10.1371/journal.pbio.1000502, <>
  13. Verena Kaynig, Thomas Fuchs, Joachim M. Buhmann (2010), "Neuron Geometry Extraction by Perceptual Grouping in ssTEM Images", CVPR, <>
  14. Longair Mark, Baker DA, Armstrong JD. (2011), "Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes.", Bioinformatics, <>
  15. Federici Fernán, Dupuy Lionel, Laplaze Laurent, Heisler Marcus, Haseloff Jim. (2012), "Integrated genetic and computation methods for in planta cytometry", Nature Methods advance online publication, <>
  16. Stephan Saalfeld, Richard Fetter, Albert Cardona, and Pavel Tomancak (2012), "Elastic volume reconstruction from series of ultra-thin microscopy sections", Nature Methods 9(7), doi:10.1038/nmeth.2072, <>
  17. Albert Cardona and Pavel Tomancak (2012), "Current challenges in open-source bioimage informatics", Nature Methods 9(7): 661–665, <>
  18. Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney J. Douglas (2012), "TrakEM2 Software for Neural Circuit Reconstruction", PLoS One 7(6): e38011, doi:doi:10.1371/journal.pone.0038011, <>
  19. Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld (2012), "ImgLib2 – Generic Image Processing in Java", Bioinformatics 28(22): 3009-3011, <>
  20. Pitrone P. G., Schindelin J., Stuyvenberg L., Preibisch S., Weber M.; Eliceiri K. W., Huisken J., Tomancak P. (2013), "OpenSPIM: an open access light sheet microscopy platform", Nature Methods, <>
  21. Shivanandan A.; Radenovic A., Sbalzarini I. F. (2013), "MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis", BMC Bioinformatics 14: 1-10, <>
  22. Krull, A., Steinborn A., Ananthanarayanan V., Ramunno-Johnson D., Petersohn U., Tolic-Norrelykke I. M. (2014), "A divide and conquer strategy for the maximum likelihood localization of low intensity objects.", Optics Express 22 (1): 210-228, <>