R Neuron Analysis Suite provides functions to read/write/analyse neuroanatomical data
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README.md

NB most AnalysisSuite functionality has been superseded by the much more modern nat R package however this code is still of more than historical interest since a small amount of functionality has yet to be ported to nat.

This package provides numerous functions for reading/writing and analysing neuroanatomical data in R. It is an update to accompany the paper:

Cachero, Ostrovsky et al., Sexual Dimorphism in the Fly Brain, Current Biology (2010), doi:10.1016/j.cub.2010.07.045

http://dx.doi.org/10.1016/j.cub.2010.07.045

of software first released for the paper:

"Comprehensive Maps of Drosophila Higher Olfactory Centers: Spatially Segregated Fruit and Pheromone Representation" Cell (2007), doi:10.1016/j.cell.2007.01.040 by Gregory S.X.E. Jefferis*, Christopher J. Potter* Alexander M. Chan, Elizabeth C. Marin Torsten Rohlfing, Calvin R. Maurer, Jr., and Liqun Luo

http://dx.doi.org/10.1016/j.cell.2007.01.040

R Install

Make sure you have a recent version of R installed (R>=2.15.1 recommended). Choose from one of the 3 install methods below and then see Running AnalysisSuite in R.

Easy Install

This is the recommended installation method if you just want to try this out. This code changes frequently, so for regular use, the Developer install is recommended.

  • Start R
  • source("http://flybrain.mrc-lmb.cam.ac.uk/R/AnalysisSuite/WebInstall.R")
    • You will be asked to choose an install/download location for the source code
    • R unfortunately doesn't have a function to choose a directory, so once you have selected your directory you will have to type a fake filename and then click "Save"
  • R will download my code and install a lot of required packages
  • Now go to Running AnalysisSuite in R

Manual Install

You should only need do this if the Easy Install fails

  • Download this repository as zip file
  • Unzip the zip file in /path/to/some/sensible/directory
  • Start R
  • Source /path/to/some/sensible/directory/AnalysisSuite/R/Install.R
    • Either use the File ... Source File menu and choose the file in the GUI
    • or source('/path/to/some/sensible/directory/AnalysisSuite/R/Install.R') at the command line
  • Now go to Running AnalysisSuite in R

Developer Install

This is strongly recommended if you plan to use this code on a regular basis

  • Make sure you have a recent version of R installed (R>=2.15.1 recommended)
  • Install git if you don't already have it
  • In a shell/terminal session
    • cd /path/to/some/sensible/directory
    • git clone https://github.com/jefferis/AnalysisSuite.git
  • Start R
  • source('/path/to/some/sensible/directory/AnalysisSuite/R/Install.R')
  • Now go to Running AnalysisSuite in R

Running AnalysisSuite in R

  • You can now start AnalysisSuite (in this and future R sessions) by doing source(getOption('gjanalysissuite.startup'))
  • See our wiki for further details.

Moving the location of AnalysisSuite

If you move the AnalysisSuite directory on your filesystem just source AnalysisSuite/R/Install.R again to update the path to AnalysisSuite.

Amira Installation

There are a few useful Amira scripts located in the amira subdirectory.

  • See instructions in the readme in amira subdirectory
  • Essentially run Install.hx script