R Package for use with rcatmaid and nat. catnat provides some higher level analysis function for, for example, clustering synapses within a neuron’s tree structure, clustering together neurons by synapse position in 3D space and splitting a neuron into different compartments (e.g. axon-dendrite-primary neurite) and visualising these splits and clusters. The packages remains heavily in development.

## What’s in the package currently?

# install
if (!require("devtools")) install.packages("devtools")
devtools::install_github("alexanderbates/catnat")

# use
library(catnat)

# some useful functions
?seesplit3d
?flow.centrality
?get.synapses
?cluster.by.synapses

Note: Installation depends on the devtools package. Windows users may need to install Rtools.

## Acknowledgements

catnat depends on rcatmaid and nat, which were developed principally by Greg Jefferis.

rcatmaid is based on python code presently visible at:

by Albert Cardona and Philipp Schlegel. Released under the GPL-3 license.