Fiji Publications

Publications introducing Fiji

• The primary reference for citing Fiji is the paper presented in Nature Methods Focus on Bioimage Informatics in July 2012¹.

• 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 presented publicly for the first time on the ImageJ User and Developer Conference in November 2008³.

• 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

• Stitching⁶

• Tracking⁷

• 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

• Lens correction algorithm fully integrated into TrakEM2 was published in Journal of Structural Biology.¹²

• TrakEM2 finally got its well deserved primary reference through the PLoS Biology paper on neuronal architecture of the fruitfly brain.¹³

• The Trainable Segmentation Plugin is inspired by a CVPR publication on segmentation of neuronal membranes in TEM images. ¹⁴

• 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!

• The elastic alignment method available in Fiji and TrakEM2 has been published in Nature Methods.¹⁷

• 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.

• Low Light Tracking Tool²² by Alex Krull from Iva Tolic lab was published in Optics Express.

• The 2D and 3D Particle Tracker algorithm available in Fiji though the MOSAICsuite plugin is described in Sbalzarini and Koumoutsakos (2005²³).

• 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. (2009²⁷) and in Helmuth and Sbalzarini (2009³⁰).

• 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 (2010³¹).

• The Interaction Analysis or MosaicIA plugin is part of the MOSAICsuite and has been described in Shivanandan, Radenovic, and Sbalzarini (2013³²).

• The MOSAICsuite also contains a Background Subtractor.

• Sholl Analysis was published in Nature Methods³³

• TrackMate was published 6 years after the initial commit, in a special edition of the Methods³⁴ journal dedicated to open source software for Life Sciences.

References