Overview

The best way to explore the analysis of the neuroanatomical and electrophysiological data in this paper is to visit the documentation site for the R frulhns package.

Data

The following data is available to accompany the publication

Tabular data underlying the figures is available through a dedicated R package, frulhns hosted on github.
- The vignette for this package completely recreates the Supplemental statistics table for the paper.
- The package has been updated to work with regular R packages
- Older versions of the package requires the AnalysisSuite R codebase to be installed at a specific location (~/projects/AnalysisSuite, see github README) in order for the vignettes to be built from scratch.
- Cached versions of the vignettes (frulhns v0.4.1) are available here:
  - neurons.pdf
  - statistics.pdf
Traced Neurons
- before registration
  - amira format
  - SWC format
- after registration to IS2 template brain
  - amira format
  - swc format
3D confocal image data (on a hard drive, on request to Greg)

Electrophysiological Analysis

Analysis and plotting of electrophysiological data initially acquired with Neuromatic/Nclamp was carried out in R, primarily using a custom R package, gphys. Although I would generally recommend using the latest version available via github, to install the specific package version associated with the manuscript, do as follows:

# Start R
 
# install (one time only)
install.packages("IgorR") # code to read Igor binary files (Greg)
install.packages("STAR") # code for Spike Train Analysis from Christophe Pouzat
# download gphys package from Jefferis lab website to a temporary file
download.file('http://flybrain.mrc-lmb.cam.ac.uk/si/frulhns/gphys-0.7-1.tar.gz',tf<-tempfile(fileext='.tgz'))
# install
install.packages(tf,repos=NULL,type='source')
# clean up temp file
unlink(tf)
 
library(gphys)
# get introductory help on package
?gphys
# get help on main plot function (including examples)
?PlotRasterFromSweeps