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'' | 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/> | ||
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''' | '''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 | * Bugfix in neurite skeleton graph | ||
* SWC files for single neurites are now generated and stored | * 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.
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:
- 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.
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
