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
This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).
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 export -- Export to SONATA format (optional)
snudda simulate -- Run the network simulation using neuron
snudda analyse
snudda help me -- Show this help text
Example of a small simulation of the striatal circuitry can be found in Jupyter notebook StriatumScaffoldExample-tiny.ipynb.
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