https://github.com/int-brain-lab/viewephys

Neuropixel raw data viewer
https://github.com/int-brain-lab/viewephys

Last synced: about 1 month 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 (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-03-14T18:59:14.000Z (9 months ago)
• Last Synced: 2024-03-15T19:26:56.261Z (9 months ago)
• Language: Python
• Size: 1.98 MB
• Stars: 2
• Watchers: 28
• Forks: 0
• Open Issues: 0
• 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.

![alt text](./docs/raw_bin_viewer_destripe.png "Ephys viewer ")

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)

```

![alt text](./docs/view_rand_array.png "Ephys viewer")

    

## Contribution

Fork and PR.

Pypi Release checklist:

```shell

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/*

```