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pub:neuroanatomy:frulhns:start [2014/01/21 23:45] – [Data] jefferissi:frulhns:start [2019/06/20 08:53] (current) – [Data] jefferis
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 +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

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