ndx-bipolar-scheme Extension for NWB

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

python installation

bash $ pip install ndx-bipolar-scheme

python usage

```python import os from pynwb import NWBHDF5IO, NWBFile from pynwb.file import DynamicTableRegion from datetime import datetime from ndxbipolarscheme import BipolarSchemeTable, NdxBipolarScheme from pynwb.ecephys import ElectricalSeries

import numpy as np

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

device = nwbfile.createdevice('devicename')

electrodegroup = nwbfile.createelectrodegroup('electrodegroup', 'desc', 'loc', device=device)

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

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

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

nwbfile.addacquisition(sourceec_series)

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

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

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

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

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

nwbfile.addacquisition(ecseries)

ndxbipolarscheme = NdxBipolarScheme( bipolarschemetables=[bipolarschemetable], source=sourceecseries ) nwbfile.addlabmetadata(ndxbipolar_scheme)

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

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

os.remove('test_nwb.nwb') ```

MATLAB usage

```matlab nwb = NwbFile( ... 'sessiondescription', 'mouse in open exploration',... 'identifier', 'Mouse5Day3', ... 'sessionstarttime', datetime(2018, 4, 25, 2, 30, 3), ... 'generalexperimenter', 'My Name', ... % optional 'generalsessionid', 'session1234', ... % optional 'generalinstitution', 'University of My Institution', ... % optional 'generalrelated_publications', 'DOI:10.1016/j.neuron.2016.12.011'); % optional

nshanks = 4; nchannelspershank = 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'); devicename = 'array'; nwb.generaldevices.set(devicename, device); devicelink = types.untyped.SoftLink(['/general/devices/' devicename]); for ishank = 1:nshanks groupname = ['shank' num2str(ishank)]; nwb.generalextracellularephys.set(groupname, ... types.core.ElectrodeGroup( ... 'description', ['electrode group for shank' num2str(ishank)], ... 'location', 'brain area', ... 'device', devicelink)); groupobjectview = types.untyped.ObjectView( ... ['/general/extracellularephys/' groupname]); for ielec = 1:nchannelspershank tbl = [tbl; {5.3, 1.5, 8.5, NaN, 'unknown', 'unknown', ... groupobjectview, [group_name 'elec' num2str(ielec)]}]; end end

electrodetable = util.table2nwb(tbl, 'all electrodes'); nwb.generalextracellularephyselectrodes = electrodetable; electrodesobjectview = types.untyped.ObjectView( ... '/general/extracellularephys/electrodes');

electrodetableregion = types.hdmfcommon.DynamicTableRegion( ... 'table', electrodesobject_view, ... 'description', 'all electrodes', ... 'data', (0:height(tbl)-1)');

sourceelectricalseries = types.core.ElectricalSeries( ... 'startingtime', 0.0, ... % seconds 'startingtimerate', 30000., ... % Hz 'data', randn(12, 3000), ... 'electrodes', electrodetableregion, ... 'dataunit', 'volts');

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

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

anodesdata = {0, [0, 1], [0, 1]}; cathodesdata = {1, [2, 3], 2};

[anodes, anodesindex] = util.createindexedcolumn(anodesdata, ... '/general/ndxbipolarscheme/bipolarscheme', [], [], electrodesobject_view);

[cathodes, cathodesindex] = util.createindexedcolumn(cathodesdata, ... '/general/ndxbipolarscheme/bipolarscheme', [], [], electrodesobject_view);

bipolarschemetable = types.ndxbipolarscheme.BipolarSchemeTable( ... 'id', types.hdmfcommon.ElementIdentifiers('data', 0:2), ... 'description', 'my description', ... 'colnames', {'anodes', 'cathods'}, ... 'anodes', anodes, 'anodesindex', anodesindex, ... 'cathodes', cathodes, 'cathodesindex', cathodes_index);

ndxbipolarscheme = types.ndxbipolarscheme.NdxBipolarScheme(... 'bipolarscheme', bipolarschemetable, ... 'source', sourceelectricalserieslink);

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

nwbExport(nwb, 'test.nwb'); ```