ndx-probeinterface Extension for NWB
ndx-probeinterface is an extension of the NWB format to formally define information about neural probes as data types in NWB files. It comes with helper functions to easily construct ndx-probeinterface.Probe from probeinterface.Probe and vice versa.
Installation
pip install ndx_probeinterface
Usage
Going from a probeinterface.Probe/ProbeGroup object to a ndx_probeinterface.Probe object
import ndx_probeinterface
pi_probe = probeinterface.Probe(...)
pi_probegroup = probeinterface.ProbeGroup()
# from_probeinterface always returns a list of ndx_probeinterface.Probe devices
ndx_probes1 = ndx_probeinterface.from_probeinterface(pi_probe)
ndx_probes2 = ndx_probeinterface.from_probeinterface(pi_probegroup)
ndx_probes = ndx_probes1.extend(ndx_probes2)
nwbfile = pynwb.NWBFile(...)
# add Probe as NWB Devices
for ndx_probe in ndx_probes:
nwbfile.add_device(ndx_probe)
pi_probe = probeinterface.Probe(...)
pi_probegroup = probeinterface.ProbeGroup()
# from_probeinterface always returns a list of ndx_probeinterface.Probe devices
ndx_probes1 = ndx_probeinterface.from_probeinterface(pi_probe)
ndx_probes2 = ndx_probeinterface.from_probeinterface(pi_probegroup)
ndx_probes = ndx_probes1.extend(ndx_probes2)
nwbfile = pynwb.NWBFile(...)
# add Probe as NWB Devices
for ndx_probe in ndx_probes:
nwbfile.add_device(ndx_probe)
Going from a ndx_probeinterface.Probe object to a probeinterface.Probe object
import ndx_probeinterface
# load ndx_probeinterface.Probe objects from NWB file
io = pynwb.NWBH5IO(file_path, 'r', load_namespaces=True)
nwbfile = io.read()
ndx_probes = []
for device in nwbfile:
if isinstance(device, ndx_probeinterface.Probe):
ndx_probes.append(device)
# convert to probeinterface.Probe objects
pi_probes = []
for ndx_probe in ndx_probes:
pi_probe = ndx_probeinterface.to_probeinterface(ndx_probe)
pi_probes.append(pi_probe)
# load ndx_probeinterface.Probe objects from NWB file
io = pynwb.NWBH5IO(file_path, 'r', load_namespaces=True)
nwbfile = io.read()
ndx_probes = []
for device in nwbfile:
if isinstance(device, ndx_probeinterface.Probe):
ndx_probes.append(device)
# convert to probeinterface.Probe objects
pi_probes = []
for ndx_probe in ndx_probes:
pi_probe = ndx_probeinterface.to_probeinterface(ndx_probe)
pi_probes.append(pi_probe)
Future plans
- Add information about the headstage used for data acquisition
- Remove redundant information from
ElectrodeTable - Incorporate this NDX into the core NWB schema
This extension was created using ndx-template.