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.

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)

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 

note that this download includes full source code for the functions in the package along with documentation and examples.

Detailed methods are included in the manuscript supplemental information. Further information on these topics is available here

• Odour Delivery
• odorants Full list of odorants in this study
• Image Registration
• Morphological neuroanatomy in R aka AnalysisSuite