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Neo io #503

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b99d64f
start neo support
BalzaniEdoardo Oct 17, 2025
ed7dcee
NeoReader
gviejo Jan 8, 2026
a53f5fa
Merge branch 'dev' into neo-io
gviejo Jan 9, 2026
f308074
Update
gviejo Jan 10, 2026
870e6d2
update neo
gviejo Jan 12, 2026
0dc5e61
Fixing conflicts
gviejo Jan 28, 2026
31ee33a
Update neo
gviejo Jan 29, 2026
9c730ba
adding better docstrings
gviejo Jan 29, 2026
88b3327
update
gviejo Feb 2, 2026
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13 changes: 13 additions & 0 deletions doc/api.rst
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Expand Up @@ -70,6 +70,19 @@ Input-Ouput
NWBFile


.. currentmodule:: pynapple.io

.. rubric:: Neo Reader / LFP

.. autosummary::
:toctree: generated/
:nosignatures:
:recursive:

NeoReader
NeoSignalInterface


.. currentmodule:: pynapple.io

.. rubric:: Numpy files
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48 changes: 47 additions & 1 deletion doc/user_guide/02_input_output.md
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Expand Up @@ -13,7 +13,7 @@ kernelspec:

# Input-output & lazy-loading

Pynapple provides loaders for [NWB format](https://pynwb.readthedocs.io/en/stable/index.html#).
Pynapple provides multiple ways to load data. The two main formats are NWB and NPZ. In addition, raw LFP data can be loaded through the NEO library.

Each pynapple objects can be saved as a [`npz`](https://numpy.org/devdocs/reference/generated/numpy.savez.html) with a special structure and loaded as a `npz`.

Expand Down Expand Up @@ -42,6 +42,8 @@ import pynapple as nap
import os
import requests, math
import tqdm
import matplotlib.pyplot as plt
import numpy as np

nwb_path = 'A2929-200711.nwb'

Expand Down Expand Up @@ -133,6 +135,50 @@ z = data['z']
print(type(z.d))
```

## LFP loading & NEO compatibility

Raw LFP data can be loaded with pynapple through the NEO library.
Internally, pynapple uses the NEO raw IO classes to read the data and convert them to one of the pynapple time series object.
This is done through the class [`nap.NeoReader`](pynapple.io.neo.NeoReader).

See here the [list of supported formats](https://neo.readthedocs.io/en/stable/rawiolist.html).


Here is a minimal working example :

```{code-cell} ipython3
:tags: [hide-cell]
import urllib
distantfile = "https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/plexon/File_plexon_3.plx"
urllib.request.urlretrieve(distantfile, "File_plexon_3.plx")
```

```{code-cell} ipython3
:tags: [hide-output]
data = nap.NeoReader("File_plexon_3.plx", format="PlexonIO");
```
```{code-cell} ipython3
print(data)
```

```{code-cell} ipython3
lfp = data['TsdFrame 0: V']
spikes = data['TsGroup']
```

```{code-cell} ipython3
fig = plt.figure()
ax1 = fig.add_subplot(2, 1, 1)
ax2 = fig.add_subplot(2, 1, 2)
ax1.plot(lfp.t, lfp.d[:])
ax1.set_xlabel("Time (s)")
colors = plt.cm.jet(np.linspace(0, 1, len(spikes)))
ax2.eventplot([spikes[i].t for i in spikes.keys()], colors=colors)
ax2.set_xlabel("Time (s)")
plt.tight_layout()
plt.show()
```

## Saving as NPZ

Pynapple objects have [`save`](pynapple.Tsd.save) methods to save them as npz files.
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2 changes: 2 additions & 0 deletions pynapple/io/__init__.py
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@@ -1,4 +1,6 @@
from .folder import Folder
from .interface_npz import NPZFile
from .interface_nwb import NWBFile
from .interface_neo import NeoReader, NeoSignalInterface
from .misc import append_NWB_LFP, load_eeg, load_file, load_folder, load_session

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