https://github.com/int-brain-lab/viewephys
Neuropixel raw data viewer
https://github.com/int-brain-lab/viewephys
Last synced: 3 months ago
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Neuropixel raw data viewer
- Host: GitHub
- URL: https://github.com/int-brain-lab/viewephys
- Owner: int-brain-lab
- License: mit
- Created: 2022-02-13T09:53:28.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-12-06T17:51:01.000Z (7 months ago)
- Last Synced: 2025-04-13T05:22:55.462Z (3 months ago)
- Language: Python
- Size: 1.95 MB
- Stars: 3
- Watchers: 25
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.cff
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README
# viewephys
Neuropixel raw data viewer
## Installation
`pip install viewephys`
Alternatively, in development mode:
```shell
git clone https://github.com/int-brain-lab/viewephys.git
cd viewephys
pip install -e .
```
### Supported environments
This is compatible with the [IBL environment](https://github.com/int-brain-lab/iblenv)
Otherwise, you can create a new environment as such:
```shell
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.
Alternatively you can point the viewer to a specific file using the command line:
```shell
viewphys -f /path/to/raw.bin
```
### Load in a numpy array or slice
```python
# 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:
```shell
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/*
```