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 data through the GUI

Activate your environment and type viewephys. Use File > open > SpikeGLX to load a neuropixel binary file, or File > open > Open Ephys to select an Open Ephys folder (containing structure.oebin). The GUI will prompt you to select a specific recording and data stream if multiple exist. File > open > NWB loads an NWB file containing an electrical series. If the file holds several electrical series you are prompted to select one.

For recordings without probe information, Probe > Load from probeinterface library allows for attaching probe geometries of different manufacturers and models from the probeinterface library (fetched online) to recordings. Channels are then shown at their positions on the probe, and can be spatially sorted.

Visualize raw binary file through the command line

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

viewephys can be used through the Python console or iPython, allowing you to create multiple instances of the viewer at once.

# 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)

# We can open multiple windows at once, but they must have different titles
data2 = data * 50
ve2 = viewephys(data, fs=fs, title="plot 2")

Note if you are running through a script, you need to instantiate the Qt application yourself:

Opening a binary file through a script

from viewephys.gui import EphysBinViewer, create_app

app = create_app()

viewer = EphysBinViewer(r"C:\Users\Joe\Desktop\1119617_LSE1_shank12_g0_imec0\1119617_LSE1_shank12_g0_t0.imec0.ap.bin")

app.exec()

Load in a numpy array or slice through a script

import numpy as np
from viewephys.gui import viewephys, create_app

app = create_app()

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)
ve2 = viewephys(data * 50, fs=fs, title="plot 2")

app.exec()

Contribution

Fork and PR.

Pypi Release checklist:

ruff check
rm -fR dist
rm -fR .pdm-build
pdm publish
#twine upload --repository-url https://test.pypi.org/legacy/ dist/*