ndx-simulation-output Extension for NWB:N

An extension for output data of large-scale simulations

Developed in collaboration between the Soltesz lab and the Allen Institute during NWB Hackathon #4 by Ben Dichter*, Kael Dai*, Aaron Milstein, Yazan Billeh, Andrew Tritt, Jean-Christophe Fillion-Robin, Anton Akhipov, Oliver Ruebel, Nicholas Cain, Kristofer Bouchard, and Ivan Soltesz

This extension defines two NWB neuorodata_types, CompartmentSeries and Compartments. CompartmentSeries stores continuous data (e.g. membrane potential, calcium concentration) from many compartments of many cells, and scales to hundreds of thousands of compartments. Compartments stores the meta-data associated with those compartments, and is stored in SimulationMetaData.

Guide

python

installation

pip install ndx-simulation-output

usage

from pynwb import NWBHDF5IO, NWBFile
from datetime import datetime
from ndx_simulation_output import CompartmentSeries, Compartments, SimulationMetaData
import numpy as np


compartments = Compartments()
compartments.add_row(number=[0, 1, 2, 3, 4], position=[0.1, 0.2, 0.3, 0.4, 0.5])
compartments.add_row(number=[0], position=[np.nan])

nwbfile = NWBFile('description', 'id', datetime.now().astimezone())

nwbfile.add_lab_meta_data(SimulationMetaData(compartments=compartments))
cs = CompartmentSeries('membrane_potential', np.random.randn(10, 6),
                       compartments=compartments, unit='V', rate=100.)
nwbfile.add_acquisition(cs)

with NWBHDF5IO('test_compartment_series.nwb', 'w') as io:
    io.write(nwbfile)

conversion from SONTATA:

from ndx_simulation_output.io import sonata2nwb

sonata2nwb('sonata_fpath', 'save_path')

MATLAB

installation

command line:

git clone https://github.com/bendichter/ndx-simulation-output.git

in matlab:

generateExtension('/path/to/ndx-simulation-output/spec/ndx-simulation-output.namespace.yaml');

usage

nwb = nwbfile()

[number, number_index] = util.create_indexed_column( ...
    {[0, 1, 2, 3, 4], 0}, '/acquisition/compartments/number');

[position, position_index] = util.create_indexed_column( ...
    {[0.1, 0.2, 0.3, 0.4, 0.5], 0}, '/acquisition/compartments/position');

compartments = types.ndx_simulation_output.Compartments( ...
    'colnames', {'number', 'position'}, ...
    'description', 'membrane potential from various compartments', ...
    'id', types.core.ElementIdentifiers('data', int64(0:5)));

compartments.position = position;
compartments.position_index = position_index;
compartments.number = number;
compartments.number_index = number_index;

membrane_potential = types.ndx_simulation_output.CompartmentSeries( ...
    'data', randn(10,6), ...
    'compartments', types.untyped.SoftLink('/acquisition/compartments'), ...
    'data_unit', 'V', ...
    'starting_time_rate', 100., ...
    'starting_time', 0.0);
    
simulation = types.ndx_simulation_output.SimulationMetaData('compartments', compartments);
    
nwb.general.set('simulation', simulation);

nwb.acquisition.set('membrane_potential', membrane_potential);

Talks

Ben Dichter*, Kael Dai*, Aaron Milstein, Yazan Billeh, Andrew Tritt, Jean-Christophe Fillion-Robin, Anton Akhipov, Oliver Ruebel, Nicholas Cain, Kristofer Bouchard, Ivan Soltesz. NWB extension for storing results of large-scale neural network simulations. NeuroInformatics. Montreal, Canada (2018). video.