mnTools

This is a toolbox for dealing with neuronal morphology. It allows the importation of '.swc' and BBP '.h5' morphology files, the individual and population analysis (and figure generation) of the morphologies; the extraction of parameter/local measure relationships, and the algorithmic generation ("synthesis") of virtual neurons.

The code is currently in MATLAB, but I am slowly working to port it to Python.

Feel free to contact me with any questions: [email protected]

Using mnTools

You will need to clone this repository, start MATLAB, change directories to mnTools/mnHelp, and execute mnaddpaths:

git clone https://github.com/joewgraham/mnTools.git
[start MATLAB]
cd mnTools/mnHelp; mnaddpaths;

This will add the necessary mnTools paths to MATLAB and put you back in the main mnTools directory.

Now we will import and analyze a few populations of morphologies.

mnimport('real', 'mnInput/mns_real_virtual/real_burke/')
mnimport('virtual_a', 'mnInput/mns_real_virtual/virtual_a/')
mnimport('virtual_b', 'mnInput/mns_real_virtual/virtual_b/')
mnimport('virtual_g', 'mnInput/mns_real_virtual/virtual_g/')

Now we will explore a real population and compare real and virtual populations.

mnfigures(real_analysis)
mnfigures(real_analysis, virtual_a_analysis)
mnfigures(real_analysis, virtual_b_analysis)
mnfigures(real_analysis, virtual_g_analysis)