elmr

Provides tools to move between adult brain EM and light level data, emphasising the interaction between the CATMAID web application and the R Neuroanatomy Toolbox package. See also https://github.com/saalfeldlab/elm, from which this package borrows both a name and uses data.

Quick Start

For the impatient ...

# install
if (!require("devtools")) install.packages("devtools") 
devtools::install_github("jefferis/elmr")

# use
library(elmr)

# run examples 
example("open_fafb")

# get overview help for package 
?elmr 

# help for functions/data 
?FAFB
?fetchn_fafb
?nblast_fafb
?open_fafb
?xform_brain
?stitch_neurons
?tpsreg

Installation

Currently there isn't a released version on CRAN.

Development version

You can use the devtools package to install the development version:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("jefferis/elmr")

# to transform skeletons to template brains other than JFRC2013, you also need
# a CMTK installation (see https://github.com/jefferis/nat/#external-dependencies)
# and to download some additional bridging registrations.
library(nat.flybrains)
download_jefferislab_registrations()

Note that this should also install the latest version of the necessary dependencies. To carry out nblast comparisons with flycircuit.tw neurons, you may need to install optional dependencies by installing as follows:

devtools::install_github("jefferis/elmr", dependencies=TRUE)

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

Updating

elmr and its dependencies are still under fairly heavy development. You can conveniently bring the devlopment versions up to date by doing:

devtools::update_packages("elmr", dependencies = TRUE)