ibl-neuropixel 0.3.0

Collection of tools for Neuropixel 1.0 and 2.0 probes data

ibl-neuropixel

Collection of tools to handle Neuropixel 1.0 and 2.0 data (documentation coming soon...)

Installation

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 neurodsp.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 destipe 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:

flake8
rm -fR dist
rm -fR build
python setup.py sdist bdist_wheel
twine upload dist/*
#twine upload --repository-url https://test.pypi.org/legacy/ dist/*