From MiToBo

Jump to: navigation, search

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


The R software environment ( 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. 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


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
Personal tools