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pub:neuroanatomy:frulhns:start [2013/12/30 19:02] – [Data] jefferispub:neuroanatomy:frulhns:start [2014/01/21 23:45] – [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 
- 
-====== Data ====== 
-The following data will be made available on publication 
- 
-  * Tabular data underlying the figures is being made available through a dedicated R package, [[https://github.com/jefferis/frulhns|frulhns]] available on github. 
-    * The vignette for this package completely recreates the Supplemental statistics table for the paper. 
-    * The current version 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 (v0.2.1) 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]] 
-  * [[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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