Applications/NeuronAnalyzer2D: Difference between revisions

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To save these variables permanently, copy the commands above to your local .bashrc file.
To save these variables permanently, copy the commands above to your local .bashrc file.
Finally the Bioconductor package [http://www.bioconductor.org/packages/release/bioc/html/xcms.html xcms] must be installed.<br/>


'''Note:''' The application is currently only available on Linux OS.<br/>
'''Note:''' The application is currently only available on Linux OS.<br/>
Current version of ''Neuron Analyzer 2D'' uses R version 3.0.2 (2013-09-25) with rJava_0.9-5 (jri_0.5-5)
Current version of ''Neuron Analyzer 2D'' was tested with R version 3.1.0 (2014-04-10) with rJava_0.9-6 (2013-12-23).


'''Example images'''<br/>
'''Example images'''<br/>
[http://www.informatik.uni-halle.de/mitobo/downloads/neuron_examples.zip Neuron example images]
[http://www.informatik.uni-halle.de/mitobo/downloads/neuron_examples.zip Neuron example images]
=== Updates ===
----<br>
'''June 2014''' (since MiToBo version [[Downloads | 1.4]])
* Updated rJava from rJava_0.9-5 to rJava_0.9-6
'''February 2014''' (since MiToBo version [[Downloads | 1.3]])
* Bugfix in neurite skeleton graph
* SWC files for single neurites are now generated and stored

Latest revision as of 08:06, 23 June 2015



Neuron Analyzer 2D

The Neuron Analyzer 2D is available since release version 1.1 of MiToBo.

NeuronAnalyzer2D.png


Published in:
D. Misiak, S. Posch, .M. Lederer, C. Reinke, S. Hüttelmaier and B. Möller,
"Extraction of protein profiles from primary neurons using active contour models and wavelets".
Journal of Neuroscience Methods, Volume 225, Pages 1-12, 30 March 2014.

Name of Plugin/Operator:
NeuronAnalyzer2D (since MiToBo version 1.1)

Main features:

  • Neuron boundary detection based on active contours
  • Identification of structural neuron parts, like soma, neurites and growth cones
  • Morphology analysis, e.g., neurite length, average neurite width, number of branch and end points, growth cone size and shape roundness, etc.
  • Extraction of molecular profiles from fluorescently labeld molecules
  • Detection of molecular particles, for example FISH data

Installation:

The R software environment (http://www.r-project.org/) must be installed to use the Neuron Analyzer 2D.
If R is installed on the system, two environment variables must be set. Perform the following steps on the commandline to set the variables:

  1. export R_HOME="/usr/lib/R" # path to your R installation
  2. export R_SCRIPTS="/path/to/ImageJ/share/scripts/R" # path to the R scripts, shipped with MiToBo zip file
  3. libjri.so must be in the LD_LIBRARY_PATH

To save these variables permanently, copy the commands above to your local .bashrc file.

Finally the Bioconductor package xcms must be installed.

Note: The application is currently only available on Linux OS.
Current version of Neuron Analyzer 2D was tested with R version 3.1.0 (2014-04-10) with rJava_0.9-6 (2013-12-23).

Example images
Neuron example images


Updates



June 2014 (since MiToBo version 1.4)

  • Updated rJava from rJava_0.9-5 to rJava_0.9-6

February 2014 (since MiToBo version 1.3)

  • Bugfix in neurite skeleton graph
  • SWC files for single neurites are now generated and stored