shruti1210 / snudda

Create realistic networks of neurons, synapses placed using touch detection between axons and dendrites

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 [email protected]

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