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Add new catalog entry for ndx-probeinterface (#41)
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khl02007 authored Jul 25, 2024
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58 changes: 58 additions & 0 deletions ndx-probeinterface/README.md
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# 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
```python
pip install ndx_probeinterface
```

## Usage

### Going from a `probeinterface.Probe`/`ProbeGroup` object to a `ndx_probeinterface.Probe` object
```python
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)
```

### Going from a `ndx_probeinterface.Probe` object to a `probeinterface.Probe` object
```python
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)
```

## 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](https://github.com/nwb-extensions/ndx-template).
8 changes: 8 additions & 0 deletions ndx-probeinterface/ndx-meta.yaml
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name: ndx-probeinterface
version: 0.1.0
src: https://github.com/SpikeInterface/ndx-probeinterface
pip: https://pypi.org/project/ndx-probeinterface/
license: MIT
maintainers:
- alejoe91
- khl02007

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