Collection of tools for Neuropixel 1.0 and 2.0 probes data
Project description
ibl-neuropixel
Collection of tools to handle Neuropixel 1.0 and 2.0 data (documentation coming soon...)
Installation
Minimum Python version supported is 3.10
pip install ibl-neuropixel
Destriping
Getting started
This relies on a fast fourier transform external library: pip install pyfftw.
Minimal working example to destripe a neuropixel binary file.
from pathlib import Path
from ibldsp.voltage import decompress_destripe_cbin
sr_file = Path('/datadisk/Data/spike_sorting/pykilosort_tests/imec_385_100s.ap.bin')
out_file = Path('/datadisk/scratch/imec_385_100s.ap.bin')
decompress_destripe_cbin(sr_file=sr_file, output_file=out_file, nprocesses=8)
Viewer
The best way to look at the results is to use viewephys, open an ephys viewer on the raw data.
- tick the destripe box.
- move to a desired location in the file
- ctr+P will make the gain and axis the same on both windows
You can then move within the raw data file.
White Paper
The following describes the methods implemented in this repository. https://doi.org/10.6084/m9.figshare.19705522
Contribution
Pypi Release checklist:
- Edit the version number in
setup.py, and add release notes inrelease_notes.md
flake8
tag=X.Y.Z
git tag -a $tag
git push origin %tag
Create new release with tag X.Y.Z (will automatically publish to PyPI)
Release history Release notifications | RSS feed
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