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Plot and analyse neurons skeletonised from image data released by FlyCircuit.


Currently there isn’t a released version on CRAN, but you can use the devtools package to install the development version:

# if necessary
if(!requireNamespace('devtools')) install.packages("devtools")
devtools::install_github("natverse/flycircuit", dependencies=TRUE)

Note: Windows users need Rtools and devtools to install this way.

Getting Started

Take a look at the package vignette (also available in fullly processed format through R’s help system).

Getting the data

We have pre-packaged a complete registered/skeletonised version of 16129 neurons from the flycircuit dataset. We are also distributing the all by all NBLAST scores for these neurons. Further details are available at

You can get the data like so:


You can also read individual skeletons hosted on the FlyCircuit website:

You could read all skeletons like so:

Acknowledging the data and tools

Any work that uses data from this package should cite

(for the original image data)

Chiang, Ann-Shyn, Chih-Yung Lin, Chao-Chun Chuang, Hsiu-Ming Chang, Chang-Huain Hsieh, Chang-Wei Yeh, Chi-Tin Shih, et al. 2011. Three-Dimensional Reconstruction of Brain-Wide Wiring Networks in Drosophila at Single-Cell Resolution. Current Biology 21(1):1–11. doi: 10.1016/j.cub.2010.11.056

(for the automated traced neuronal skeletons)

Lee, Ping-Chang, Chao-Chun Chuang, Ann-Shyn Chiang, and Yu-Tai Ching. 2012. High-Throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications. PLoS Computational Biology 8(9):e1002658. doi: 10.1371/journal.pcbi.1002658

(for the package, cell type annotations and NBLAST results)

Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE. (2016) NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases. Neuron 91(2):293-311. doi: 10.1016/j.neuron.2016.06.012 (URL:

This package was created by James Manton, Marta Costa, Alexander Shakeel Bates and Gregory Jefferis.

You can obtain a citation for this package as:

citation(package = "flycircuit")