catalystneuro / ndx-probe-interface

Neurodata Without Borders (NWB) extension for probe shape information

ndx-probe-interface Extension for NWB

SpikeInterface outputs information about probes, including the probe_planar_contour which defines the polygon shape of the electrodes themselves, so to record this information in NWB, one could use the ndx-probe-interface to generate a structure that holds these details of the electrode.

Installation

cd ndx-probe-interface
pip install .

Usage

import ndx_probe_interface as npi

probe_name = "my probe" 

# On an NWB file without an ElectrodeGroup in place yet, add the Probe Device
nwbfile.add_device(npi.Probe(name=probe_name, probe_planar_contour=np.empty((1, 1)))) 

# Create the ElectrodeGroup that uses the Probe Device we just added 
nwbfile.create_electrode_group(name="my electrode group", description="a description", location='', device=nwbfile.devices[probe_name])

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This extension was created using ndx-template.