ndx-probeinterface NWB扩展

ndx-probeinterface是NWB格式的扩展，用于正式在NWB文件中将有关神经探针的信息定义为数据类型。它包含辅助函数，可以轻松地将ndx-probeinterface.Probe从probeinterface.Probe构造，反之亦然。

安装

pip install ndx_probeinterface

使用方法

从probeinterface.Probe或ProbeGroup对象到ndx_probeinterface.Probe对象的转换

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)

从ndx_probeinterface.Probe对象到probeinterface.Probe对象的转换

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)

未来计划

• 添加关于用于数据采集的头端信息
• 从ElectrodeTable中删除冗余信息
• 将此NDX纳入核心NWB架构

此扩展使用ndx-template创建。