Publications

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Publications introducing Fiji

  • Fiji was prominently featured in Nature Methods review supplement on visualization [2]

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[6]
  • TrakEM2 was used and enhanced to identify neuronal lineages, and an article was published in the Journal of Neuroscience[7] about it.
  • The algorithms behind TrakEM2 registration were presented at the ISMB conference and published in Bioinformatics.[8]
  • TrakEM2 finally got its well deserved primary reference through the PLoS Biology paper on neuronal architecture of the fruitfly brain.[10]
  • 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. [12]
  • 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[13] forward. Thanks Lionel Dupuy!

References

  1. ↑ Schindelin J (November 2008). "Fiji Is Just ImageJ (batteries included)".. 
  2. ↑ 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, <http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1431.html>
  3. ↑ 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, <http://bioinformatics.oxfordjournals.org/cgi/content/full/25/11/1463>
  4. ↑ 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, <http://www3.interscience.wiley.com/journal/122393807/abstract>
  5. ↑ 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, <http://www.biomedcentral.com/1471-2105/11/274/abstract>
  6. ↑ 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, <http://www.nature.com/nmeth/journal/v7/n6/full/nmeth0610-418.html>
  7. ↑ 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, <http://www.jneurosci.org/cgi/content/full/30/22/7538>
  8. ↑ 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, <http://bioinformatics.oxfordjournals.org/cgi/content/full/26/12/i57?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=Saalfeld&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT>
  9. ↑ 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, <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WM5-50106VP-1&_user=10&_coverDate=08/31/2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=1d165c88d80bf6db0a4d91f9dafa48c7>
  10. ↑ 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, <http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000502>
  11. ↑ Verena Kaynig, Thomas Fuchs, Joachim M. Buhmann (2010), "Neuron Geometry Extraction by Perceptual Grouping in ssTEM Images", CVPR, <http://kaynig.de/kaynig_cvpr2010.pdf>
  12. ↑ Longair Mark, Baker DA, Armstrong JD. (2011), "Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes.", Bioinformatics, <http://bioinformatics.oxfordjournals.org/content/early/2011/07/04/bioinformatics.btr390.long>
  13. ↑ 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, <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1940.html>
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