Clone the repository.
$ git clone https://github.com/BonsaiNet/McNeuron.gitFor more information Go to the following notebook with title: Download neuromorpho.org
For more information Go to the following notebook with title: How to use McNeuron to depict a neuron
For more information Go to the following notebook with title: Extracting features
We can generate samples of different cell types by McNeuron. Technically, it uses Reversible-jump Markov Chain Monte Carlo (RJMCMA) generating morphologies. It extracts features of a database of neuron and then generates neuron with the same features. Specificaly, the algorithm starts from a simple neuron (e.g. a neuron with soma only) and perturbing it using RJMCMC and gradually enriches the morphology with the desired features (see figure below). In this framework, adding more morpgological features reasults in more realistic neurons. The main advantage of this approach is that it can generates morphologies for any cell type.
You can see a few samples here:
If you want to know more about this algorithm read the paper below: Farhoodi, Roozbeh, and Konrad P. Kording. "Sampling Neuron Morphologies." bioRxiv (2018): 248385.
To run the algorithm follow the script go to
https://github.com/BonsaiNet/McNeuron/blob/master/Generating%20Neurons%20with%20MCMC.ipynb
If you used this package, we really appriciate if you cite our paper: Farhoodi, Roozbeh, and Konrad P. Kording. "Sampling Neuron Morphologies." bioRxiv (2018): 248385.
Contact: Roozbeh Farhoodi [roozbehfarhoodi@gmail.com]