Create realistic networks of neurons, synapses placed using touch detection between axons and dendrites.
Project description
Snudda
Create realistic networks of neurons, synapses placed using touch detection between axons and dendrites
Contact details
Johannes Hjorth, Royal Institute of Technology (KTH) Human Brain Project 2019 hjorth@kth.se
Funding
Horizon 2020 Framework Programme (785907, HBP SGA2); Horizon 2020 Framework Programme (945539, HBP SGA3); Vetenskapsrådet (VR-M-2017-02806); Swedish e-science Research Center (SeRC); KTH Digital Futures.
Installation
https://github.com/Hjorthmedh/Snudda/wiki/1.-User-installation
Jupyter Notebook examples
https://github.com/Hjorthmedh/Snudda/tree/master/examples/notebooks
Usage
Usage:
snudda init --size XXX -- Creates an a json config file
snudda place -- Cell placement within volumes specified
snudda detect [--hvsize hyperVoxelSize] -- Touch detection of putative synapses
snudda prune [--mergeonly] -- Prune the synapses
snudda input [--input yourInputConfig] -- Setup the input, obs you need to manually pick a input config file
snudda simulate -- Run the network simulation using neuron
snudda analyse
snudda help me -- Show this help text
Project details
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