Note
Click here to download the full example code
Load an Allen Brain Map NWB into pynapple
In this example, we show how to load into pynapple an NWB directly downloaded from the Allen Brain Map.
Intracellular recordings NWBs and pynapple
NWB files containing intracellular recordings cannot be imported directly into pynapple. This is because pynapple requires a continuous time axis, but these experiments are typically divided into sweeps, with each sweep starting at t = 0 seconds.
At this link,
we provide the load_allen.py module for loading intracellular recordings into pynapple.
It works by concatenating all sweeps together and adding a fixed inter-trial interval between sweeps to
create a continuous time axis.
For this example, let's assume that you download the dataset used in the tutorial directly from the Allen website:
https://celltypes.brain-map.org/experiment/electrophysiology/478498617
To load it into pynapple, you can run the following code,
# The "load_allen.py" module is in
# https://github.com/pynapple-org/single-cell-neuropython-workshop-2024/blob/main/docs/examples/load_allen.py
from load_allen import load_to_pynapple
# replace this with the path to the nwb data
path = "478498615_ephys.nwb"
# this will return the pynapple representation of the data.
# note: that we used the same naming as in "tutorial_pynapple_nemos_single_cell_full.py"
spikes, epochs, current, voltage, sweep_metadata = load_to_pynapple(path)
Total running time of the script: ( 0 minutes 0.000 seconds)
Download Python source code: example_load_to_pynapple.py