ndx-bipolar-scheme Extension for NWB

Structure for storing the bipolar schema of a recording in an NWB file.

python installation

$ pip install ndx-bipolar-scheme

python usage

import os
from pynwb import NWBHDF5IO, NWBFile
from pynwb.file import DynamicTableRegion
from datetime import datetime
from ndx_bipolar_scheme import BipolarSchemeTable, NdxBipolarScheme
from pynwb.ecephys import ElectricalSeries

import numpy as np

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

device = nwbfile.create_device('device_name')

electrode_group = nwbfile.create_electrode_group('electrode_group',
                                                 'desc', 'loc', device=device)

for i in np.arange(20.):
    nwbfile.add_electrode(i, i, i, np.nan, 'loc', 'filt', electrode_group)

electrodes = DynamicTableRegion(
    name='electrodes',
    data=np.arange(0, 3),
    description='desc',
    table=nwbfile.electrodes,
)

source_ec_series = ElectricalSeries(
    name='source_ec_series',
    description='desc',
    data=np.random.rand(100, 3),
    rate=1000.,
    electrodes=electrodes,
)

nwbfile.add_acquisition(source_ec_series)

bipolar_scheme_table = BipolarSchemeTable(
    name='bipolar_scheme', description='desc'
)

bipolar_scheme_table.add_row(anodes=[0], cathodes=[1])
bipolar_scheme_table.add_row(anodes=[0, 1], cathodes=[2, 3])
bipolar_scheme_table.add_row(anodes=[0, 1], cathodes=[2])

bipolar_scheme_table['anodes'].target.table = nwbfile.electrodes
bipolar_scheme_table['cathodes'].target.table = nwbfile.electrodes

bipolar_scheme_region = DynamicTableRegion(
    name='electrodes',
    data=np.arange(0, 3),
    description='desc',
    table=bipolar_scheme_table,
)

ec_series = ElectricalSeries(
    name='dest_ec_series',
    description='desc',
    data=np.random.rand(100, 3),
    rate=1000.,
    electrodes=bipolar_scheme_region,
)

nwbfile.add_acquisition(ec_series)

ndx_bipolar_scheme = NdxBipolarScheme(
    bipolar_scheme_tables=[bipolar_scheme_table],
    source=source_ec_series
)
nwbfile.add_lab_meta_data(ndx_bipolar_scheme)

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

with NWBHDF5IO('test_nwb.nwb', 'r', load_namespaces=True) as io:
    nwbfile = io.read()
    nwbfile.acquisition['dest_ec_series'].electrodes.table['anodes'][2]['x']

os.remove('test_nwb.nwb')

MATLAB usage

nwb = NwbFile( ...
    'session_description', 'mouse in open exploration',...
    'identifier', 'Mouse5_Day3', ...
    'session_start_time', datetime(2018, 4, 25, 2, 30, 3), ...
    'general_experimenter', 'My Name', ... % optional
    'general_session_id', 'session_1234', ... % optional
    'general_institution', 'University of My Institution', ... % optional
    'general_related_publications', 'DOI:10.1016/j.neuron.2016.12.011'); % optional

nshanks = 4;
nchannels_per_shank = 3;
variables = {'x', 'y', 'z', 'imp', 'location', 'filtering', 'group', 'label'};
tbl = cell2table(cell(0, length(variables)), 'VariableNames', variables);
device = types.core.Device(...
    'description', 'the best array', ...
    'manufacturer', 'Probe Company 9000');
device_name = 'array';
nwb.general_devices.set(device_name, device);
device_link = types.untyped.SoftLink(['/general/devices/' device_name]);
for ishank = 1:nshanks
    group_name = ['shank' num2str(ishank)];
    nwb.general_extracellular_ephys.set(group_name, ...
        types.core.ElectrodeGroup( ...
            'description', ['electrode group for shank' num2str(ishank)], ...
            'location', 'brain area', ...
            'device', device_link));
    group_object_view = types.untyped.ObjectView( ...
        ['/general/extracellular_ephys/' group_name]);
    for ielec = 1:nchannels_per_shank
        tbl = [tbl; {5.3, 1.5, 8.5, NaN, 'unknown', 'unknown', ...
            group_object_view, [group_name 'elec' num2str(ielec)]}];
    end
end

electrode_table = util.table2nwb(tbl, 'all electrodes');
nwb.general_extracellular_ephys_electrodes = electrode_table;
electrodes_object_view = types.untyped.ObjectView( ...
    '/general/extracellular_ephys/electrodes');

electrode_table_region = types.hdmf_common.DynamicTableRegion( ...
    'table', electrodes_object_view, ...
    'description', 'all electrodes', ...
    'data', (0:height(tbl)-1)');

source_electrical_series = types.core.ElectricalSeries( ...
    'starting_time', 0.0, ... % seconds
    'starting_time_rate', 30000., ... % Hz
    'data', randn(12, 3000), ...
    'electrodes', electrode_table_region, ...
    'data_unit', 'volts');

nwb.acquisition.set('ElectricalSeries', source_electrical_series);

source_electrical_series_link = types.untyped.SoftLink( ...
    '/acquisition/ElectricalSeries');

anodes_data = {0, [0, 1], [0, 1]};
cathodes_data = {1, [2, 3], 2};

[anodes, anodes_index] = util.create_indexed_column(anodes_data, ...
    '/general/ndx_bipolar_scheme/bipolar_scheme', [], [], electrodes_object_view);

[cathodes, cathodes_index] = util.create_indexed_column(cathodes_data, ...
    '/general/ndx_bipolar_scheme/bipolar_scheme', [], [], electrodes_object_view);

bipolar_scheme_table = types.ndx_bipolar_scheme.BipolarSchemeTable( ...
    'id', types.hdmf_common.ElementIdentifiers('data', 0:2), ...
    'description', 'my description', ...
    'colnames', {'anodes', 'cathods'}, ...
    'anodes', anodes, 'anodes_index', anodes_index, ...
    'cathodes', cathodes, 'cathodes_index', cathodes_index);

ndx_bipolar_scheme = types.ndx_bipolar_scheme.NdxBipolarScheme(...
    'bipolar_scheme', bipolar_scheme_table, ...
    'source', source_electrical_series_link);

nwb.general.set('ndx_bipolar_scheme', ndx_bipolar_scheme);

nwbExport(nwb, 'test.nwb');