Supplemental data to accompany:

[[http://www.cell.com/abstract/S0092-8674(13)01476-1|**A bidirectional circuit switch reroutes pheromone signals in male and female brains**]]\\
Cell, Volume 155, Issue 7, 1610-1623, 19 December 2013 [[http://dx.doi.org/10.1016/j.cell.2013.11.025|doi:10.1016/j.cell.2013.11.025]]\\
Johannes Kohl*, Aaron D. Ostrovsky*, Shahar Frechter, Gregory S.X.E. Jefferis

====== 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 [[https://jefferis.github.io/frulhns|frulhns]] package. 

====== Data ======
The following data is available to accompany the publication

  * Tabular data underlying the figures is available through a dedicated R package, [[https://github.com/jefferis/frulhns|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 [[https://github.com/jefferis/AnalysisSuite|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:
      * [[http://jefferislab.org/si/frulhns/neurons.pdf|neurons.pdf]]
      * [[http://jefferislab.org/si/frulhns/statistics.pdf|statistics.pdf]]
  * Traced Neurons
    * before registration
      * [[http://flybrain.mrc-lmb.cam.ac.uk/si/frulhns/traces.zip|amira format]]
      * [[http://flybrain.mrc-lmb.cam.ac.uk/si/frulhns/traces.swc.zip|SWC format]]
    * after registration to IS2 template brain
      * [[http://flybrain.mrc-lmb.cam.ac.uk/si/frulhns/traces.IS2.zip|amira format]]
      * [[http://flybrain.mrc-lmb.cam.ac.uk/si/frulhns/traces.IS2.swc.zip|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, [[https://github.com/jefferis/gphys|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:

<code python>
# 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 
</code>

note that this download includes full source code for the functions in the package along with documentation and examples.
====== Methods ======
Detailed methods are included in the manuscript supplemental information. Further information on these topics is available here
  * [[alex:projects:odour_presentation_system:start|Odour Delivery]]
  * [[pub:neuroanatomy:frulhns:odorants]] Full list of odorants in this study
  * [[warping_manual:start|Image Registration]]
  * [[https://github.com/jefferis/AnalysisSuite|Morphological neuroanatomy in R]] aka AnalysisSuite