The Region Competition algorithm has been published in Cardinale, Paul, and Sbalzarini and Koumoutsakos (2012 29).The Squassh workflow for segmentation and quantification of subcellular shapes in fluorescence microscopy images has been published in in Rizk et al.It optionally also corrects for the microscope PSF, providing deconvolving segmentation as described in Helmuth et al. 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 25).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. The 2D and 3D Particle Tracker algorithm available in Fiji though the MOSAICsuite plugin is described in Sbalzarini and Koumoutsakos (2005 23).Low Light Tracking Tool 22 by Alex Krull from Iva Tolic lab was published in Optics Express.OpenSPIM 21 relies heavily on Fiji for microscope operation and SPIMage processing.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. ImgLib2 was published in Bioinformatics.Albert Cardona’s TrakEM2 was published in PLoS One 19.A commentary by Albert Cardona and Pavel Tomancak discusses the impact and problems open source software development faces in academia 18.The elastic alignment method available in Fiji and TrakEM2 has been published in Nature Methods.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 16 forward.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.The Trainable Segmentation Plugin is inspired by a CVPR publication on segmentation of neuronal membranes in TEM images.TrakEM2 finally got its well deserved primary reference through the PLoS Biology paper on neuronal architecture of the fruitfly brain.Lens correction algorithm fully integrated into TrakEM2 was published in Journal of Structural Biology.The algorithms behind TrakEM2 registration were presented at the ISMB conference and published in Bioinformatics.TrakEM2 was used and enhanced to identify neuronal lineages, and an article was published in the Journal of Neuroscience 10 about it.A powerful plugin for registering SPIM (Selective Plane Illumination Microscopy) and other multi-angle image data was published in Nature Methods 9.Fiji’s 3D Viewer was published in BMC Bioinformatics 8.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).
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