View source for Applications/NeuronAnalyzer2D

<br/>
<br/>

== Neuron Analyzer 2D ==

The ''Neuron Analyzer 2D'' is available since release version 1.1 of MiToBo. [[File:NeuronAnalyzer2D.png|right|link=]]
<br/>
'''Published in:'''<br/>
''D. Misiak, S. Posch, .M. Lederer, C. Reinke, S. Hüttelmaier and B. Möller,<br/>
'''"Extraction of protein profiles from primary neurons using active contour models and wavelets"'''.<br/>
Journal of Neuroscience Methods, Volume 225, Pages 1-12, 30 March 2014.'' 

'''Name of Plugin/Operator:'''<br/>
NeuronAnalyzer2D (since MiToBo version 1.1)

'''Main features:'''<br/>
* 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:'''<br/>

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

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

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

'''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)

'''Example images'''<br/>
[http://www.informatik.uni-halle.de/mitobo/downloads/neuron_examples.zip Neuron example images]


=== Updates ===

----<br>

'''Februar 2014''' (since MiToBo version [[Downloads | 1.3]])
* Bugfix in neurite skeleton graph
* SWC files for single neurites are now generated and stored