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).A review of biological imaging software tools focusses on open source programs and Fiji is a big part of it 5.
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