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 uv pip install ibl-neuropixel

Destriping

Getting started

Compress a binary file losslessly using mtscomp

The mtscomp util implements fast chunked compression for neurophysiology data in a single shard. Package repository is here.

from pathlib import Path
import spikeglx
file_spikeglx = Path('/datadisk/neuropixel/file.imec0.ap.bin')
sr = spikeglx.Reader(file_spikeglx)
sr.compress_file()
# note: you can use sr.compress_file(keep_original=False) to also remove the orginal bin file

Reading raw spikeglx file and manipulating arrays

The mtscomp util implements fast chunked compression for neurophysiology data in a single shard. Package repository is here.

from pathlib import Path
import spikeglx

import ibldsp.voltage

file_spikeglx = Path('/datadisk/Data/neuropixel/human/Pt01.imec0.ap.bin')
sr = spikeglx.Reader(file_spikeglx)

# reads in 300ms of data
raw = sr[10_300_000:10_310_000, :sr.nc - sr.nsync].T
destripe = ibldsp.voltage.destripe(raw, fs=sr.fs, neuropixel_version=1)

# display with matplotlib backend
import ibldsp.plots
ibldsp.plots.voltageshow(raw, fs=sr.fs, title='raw')
ibldsp.plots.voltageshow(destripe, fs=sr.fs, title='destripe')

# display with QT backend
from viewephys.gui import viewephys
eqc = {}
eqc['raw'] = viewephys(raw, fs=sr.fs, title='raw')
eqc['destripe'] = viewephys(destripe, fs=sr.fs, title='destripe')

Destripe a binary file

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

Please see our contribution guidelines for details on how to contribute to this project.