Raw Neuropixel data viewer for numpy
Project description
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=3.9
conda activate viewephys
And then follow the install instructions above.
Examples
Visualize raw binary file
Activate your environment and type viewephys
, you can then load a neuropixel binary file using the file menu.
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)
Contribution
Fork and PR.
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/*
Project details
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