#Schenider 2012 imagej software registration#
#Schenider 2012 imagej software software#

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.

#Schenider 2012 imagej software software#

A commentary by Albert Cardona and Pavel Tomancak discusses the impact and problems open source software development faces in academia.

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 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.

#Schenider 2012 imagej software registration#

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 about it.A powerful plugin for registering SPIM (Selective Plane Illumination Microscopy) and other multi-angle image data was published in Nature Methods.Fiji's 3D Viewer was published in BMC Bioinformatics.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.Fiji was prominently featured in Nature Methods review supplement on visualization.Fiji was presented publicly for the first time on the ImageJ User and Developer Conference in November 2008.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 2015.

The primary reference for citing Fiji is the paper presented in Nature Methods Focus on Bioimage Informatics in July 2012.