Publications

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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.
  • 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. (2014[23]).
  • 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 (2013[24]). It optionally also corrects for the microscope PSF, providing deconvolving segmentation as described in Helmuth et al. (2009[25]) and in Helmuth and Sbalzarini (2009[26])
  • The Squassh workflow for segmentation and quantification of subcellular shapes in fluorescence microscopy images has been published in in Rizk et al. (2014[27]).
  • The Region Competition algorithm has been published in Cardinale, Paul, and Sbalzarini and Koumoutsakos (2012[28]). 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. (2009[29]) and in Helmuth and Sbalzarini (2009[30]).
  • 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 (2010[31]).

References

  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, <http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2019.html>
  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, <http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1431.html>
  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, <http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2084.html>
  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, <http://bioinformatics.oxfordjournals.org/cgi/content/full/25/11/1463>
  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, <http://www3.interscience.wiley.com/journal/122393807/abstract>
  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, <http://www.biomedcentral.com/1471-2105/11/274/abstract>
  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, <http://www.nature.com/nmeth/journal/v7/n6/full/nmeth0610-418.html>
  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, <http://www.jneurosci.org/cgi/content/full/30/22/7538>
  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, <http://bioinformatics.oxfordjournals.org/cgi/content/full/26/12/i57?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=Saalfeld&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT>
  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, <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>
  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, <http://www.plosbiology.org/article/info: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, <http://kaynig.de/kaynig_cvpr2010.pdf>
  14. 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>
  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, <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1940.html>
  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, <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2072.html>
  17. Albert Cardona and Pavel Tomancak (2012), "Current challenges in open-source bioimage informatics", Nature Methods 9(7): 661–665, <http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2082.html>
  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, <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038011>
  19. Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld (2012), "ImgLib2 – Generic Image Processing in Java", Bioinformatics 28(22): 3009-3011, <http://bioinformatics.oxfordjournals.org/content/28/22/3009>
  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, <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2507.html>
  21. 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, <http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-22-1-210&id=276396>
  22. I. F. Sbalzarini and P. Koumoutsakos. Feature point tracking and trajectory analysis for video imaging in cell biology, J. Struct. Biol., 151(2):182-195, 2005
  23. N. Chenouard et al. Objective comparison of particle tracking methods, Nature Methods, 11(3):281-289, 2014
  24. G. Paul, J. Cardinale, and I. F. Sbalzarini. Coupling image restoration and segmentation: A generalized linear model/Bregman perspective, Int. J. Comput. Vis., 104(1): 69-93, 2013
  25. J. A. Helmuth, C. J. Burckhardt, U. F. Greber, and I. F. Sbalzarini. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images, Journal of Structural Biology, 167:1–10, 2009
  26. 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.
  27. A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini. Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh Nature Protocols., 9(3): 586-596, 2014
  28. J. Cardinale, G. Paul, and I. F. Sbalzarini. Discrete region competition for unknown numbers of connected regions, IEEE Trans. Image Process., 21(8): 3531–3545, 2012
  29. J. A. Helmuth, C. J. Burckhardt, U. F. Greber, and I. F. Sbalzarini. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images, Journal of Structural Biology, 167:1–10, 2009
  30. 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.
  31. J. A. Helmuth, G. Paul, and I. F. Sbalzarini. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images, BMC Bioinformatics., 11:372, 2010
  32. A. Shivanandan, A. Radenovic, and I. F. Sbalzarini. MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis, BMC Bioinformatics., 14:349, 2013
  33. 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