About

This website accompanies the paper Neuron: Costa et al. (2016) NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases and preprint bioRxiv: Costa et al. (2014) NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases and acts as a hub for demonstrations of the core NBLAST algorithm (package nat.nblast), along with some features of the NeuroAnatomy Toolbox.

Contact

For problem-solving, or for more information beyond that contained in the manuscript, please use the nat-user google group shown in the FAQ page.

You can also contact Greg Jefferis at jefferis <at> mrc-lmb <dot> cam <dot> ac <dot> uk.

Software / data used

We used the Computational Morphometry Toolkit for image registration, particularly the munger script therein, using these scripts for template brain construction. Image processing and analysis was performed with a combination of Fiji/ImageJ and unu. Image registration and skeletonisation was coordinated using nat.as, with R being used for general analysis.

Images from FlyCircuit (Chiang et al., 2011) were obtained from the National Center for High-performance Computing and National Tsing Hua University, Hsinchu, Taiwan.

Images from FlyLight (Jenett et al., 2012) were obtained from the Janelia FlyLight Project Team at the Janelia Research Campus, Virginia, US.

Preparing own data for use with NBLAST

Protocols for immunostaining and imaging fly brains, as well as registration of the resulting images are available from Cold Spring Harbor Protocols. We recommend the use of Simple Neurite Tracer for tracing neurons from the acquired images, detailed instructions for which are available from here.

Examples with datasets from other species

We have previously explored neuronal data from other species using NBLAST and have made these analyses available through our nat.examples R package. In particular, we have looked at monarch butterfly neurons from insectbraindb.org and the zebrafish olfactory projectome from Miyasaka et al. Olfactory projectome in the zebrafish forebrain revealed by genetic single-neuron labelling, Nature Communications.