Neuron Analyzer 2D
The Neuron Analyzer 2D is available since release version 1.1 of MiToBo.
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)
- 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
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).
Neuron example images
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