catnat

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("jefferislab/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:

• https://github.com/catmaid/CATMAID/blob/master/scripts/remote/access.py
• https://github.com/catmaid/CATMAID/blob/master/django/applications/catmaid/urls.py
• https://github.com/schlegelp/CATMAID-to-Blender/blob/master/CATMAIDImport.py

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