VIOLA

Tool description

VIOLA (VIsualizer Of Layer Activity) is a tool to visualize activity in multiple 2D layers in an interactive and efficient way. It gives an insight into spatially resolved time series such as simulation results of neural networks with 2D geometry.

The usage example shows how VIOLA can be used to visualize spike data from a NEST simulation (http://nest-simulator.org/) of an excitatory and an inhibitory neuron population with distance-dependent connectivity.

Detailed documentation will be made available in the Wiki. Short usage example are shown below.

Usage example

The following description includes generation and processing of output data from a simulation of a point-neuron network with 2D geometry implemented using NEST through Python (http://www.python.org). The scripts can be found in the folder 'test_data'. These steps can be skipped, as the simulation output can already be found in 'test_data/out_raw' and 'test_data/out_proc'.

1. Generate spike data with NEST

python topo_brunel_alpha_nest.py out_raw

creates a directory 'out_raw' which contains the simulation output and a configuration file for VIOLA.

2. Visualize raw spike data

• start VIOLA (/VIOLA/index.html) in a browser (Chrome preferred), and load the configuration file 'config_raw.json'. Alternatively, adjust the parameters manually.
• upload the following files:
  • spikes-0.gdf, spikes-1.gdf
  • neuron_positions-0.dat, neuron_positions-1.dat

3. Preprocess spike data

python nest_preprocessing.py out_raw out_proc

or with OpenMPI:

mpirun -np 2 python nest_preprocessing.py out_raw out_proc

applies a spatial binning and changes the time step, output files are stored in 'out_proc'.

4. Generate LFP like signal from spike data

python fake_LFP_signal.py out_raw out_proc

5. Visualize preprocessed data

• start VIOLA and load the configuration file 'config_proc.json'
• upload the following files:
  • binned_sprates_rs_EX.dat, binned_sprates_rs_IN.dat
  • LFPdata.lfp

Simulation script dependencies

• Python 2.7.x
• numpy
• matplotlib
• scipy
• h5py
• mpi4py
• NEST 2.10.x

VIOLA-compatible browsers

• Chrome
• Opera

Authors

• Corto Carde, Johanna Senk, Espen Hagen, Benjamin Weyers