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 a name and which was used to define the landmark data sets that provide a bridge between the FAFB EM brain and light level template.

Quick Start

For the impatient ...

# install
if (!require("devtools")) install.packages("devtools") 
devtools::install_github("natverse/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("natverse/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("natverse/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 development versions up to date by doing:

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

Acknowledgements

elmr is part of a suite of R packages based on the NeuroAnatomy Toolbox
The approach to transforming data between template brains is described in

Combining genome-scale Drosophila 3D neuroanatomical data by bridging template brains James D. Manton, Aaron D. Ostrovsky, Lea Goetz, Marta Costa, Torsten Rohlfing, Gregory S. X. E. Jefferis. bioRxiv 006353; doi: 10.1101/006353
The elm tool originally used to define landmarks is in turn based on BigWarp:

JA Bogovic, P Hanslovsky, A Wong, S Saalfeld, "Robust registration of calcium images by learned contrast synthesis", In Biomedical Imaging (ISBI), 2016 IEEE 13th International Symposium on, 1123-1126, DOI: 10.1109/ISBI.2016.7493463.
Finally, the FAFB EM dataset is described in:

A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster Zhihao Zheng, J. Scott Lauritzen, Eric Perlman, Camenzind G. Robinson, Matthew Nichols, Daniel Milkie, Omar Torrens, John Price, Corey B. Fisher, Nadiya Sharifi, Steven A. Calle-Schuler, Lucia Kmecova, Iqbal J. Ali, Bill Karsh, Eric T. Trautman, John Bogovic, Philipp Hanslovsky, Gregory S. X. E. Jefferis, Michael Kazhdan, Khaled Khairy, Stephan Saalfeld, Richard D. Fetter, Davi D. Bock bioRxiv 140905; doi: 10.1101/140905

natverse / elmr