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viewephys

Neuropixel raw data viewer

Installation

pip install viewephys

Alternatively, in development mode:

git clone https://github.com/int-brain-lab/viewephys.git
cd viewephys
pip install -e .

Supported environments

This is compatible with the IBL environment

Otherwise, you can create a new environment as such:

conda create -n viewephys python=3.12
conda activate viewephys

And then follow the install instructions above.

Controls

  • ctrl + z: -3dB gain
  • ctrl + a: +3dB gain
  • ctrl + p: in multi-windows mode, link the displays (pan, zoom and gain)

Pick spikes

When the picking mode is enabled (menu pick)

  • left button click sets a point
  • shift + left button removes a point
  • control + left does not wrap on maximum around pick
  • space increments the spike group number

Examples

Visualize raw binary file

Activate your environment and type viewephys, you can then load a neuropixel binary file using the file menu.

alt text

Alternatively you can point the viewer to a specific file using the command line:

viewphys -f /path/to/raw.bin

Load in a numpy array or slice

# if running ipython, you may have to use the `%gui qt` magic command
import numpy as np
from viewephys.gui import viewephys
nc, ns, fs = (384, 50000, 30000)  # this mimics one second of neuropixel data
data = np.random.randn(nc, ns) / 1e6  # volts by default
ve = viewephys(data, fs=fs)

alt text

Contribution

Fork and PR.

Pypi Release checklist:

ruff check
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/*