https://github.com/int-brain-lab/ibl-neuropixel

Collection of tools to handle Neuropixel 1.0 and 2.0 data
https://github.com/int-brain-lab/ibl-neuropixel

Last synced: about 1 month ago
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Collection of tools to handle Neuropixel 1.0 and 2.0 data

• Host: GitHub
• URL: https://github.com/int-brain-lab/ibl-neuropixel
• Owner: int-brain-lab
• License: mit
• Created: 2022-04-18T09:47:12.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-11-01T22:48:24.000Z (about 2 months ago)
• Last Synced: 2024-11-01T23:25:19.461Z (about 2 months ago)
• Language: Python
• Size: 1.9 MB
• Stars: 12
• Watchers: 27
• Forks: 4
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

        
# ibl-neuropixel

Collection of tools to handle Neuropixel 1.0 and 2.0 data

(documentation coming soon...)

## Installation

Minimum Python version supported is 3.10

`pip install ibl-neuropixel`

## Destriping

### Getting started

This relies on a fast fourier transform external library: `pip install pyfftw`.

Minimal working example to destripe a neuropixel binary file. 

```python

from pathlib import Path

from ibldsp.voltage import decompress_destripe_cbin

sr_file = Path('/datadisk/Data/spike_sorting/pykilosort_tests/imec_385_100s.ap.bin')

out_file = Path('/datadisk/scratch/imec_385_100s.ap.bin')

decompress_destripe_cbin(sr_file=sr_file, output_file=out_file, nprocesses=8)

```

### Viewer

The best way to look at the results is to use [viewephys](https://github.com/oliche/viewephys),

open an ephys viewer on the raw data.

- tick the destripe box.

- move to a desired location in the file

- ctr+P will make the gain and axis the same on both windows

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

You can then move within the raw data file.

### White Paper

The following describes the methods implemented in this repository.

https://doi.org/10.6084/m9.figshare.19705522

## Contribution

Pypi Release checklist:

- Edit the version number in `setup.py`, and add release notes in `release_notes.md`

```shell

flake8

tag=X.Y.Z

git tag -a $tag 

git push origin %tag

```

Create new release with tag X.Y.Z (will automatically publish to PyPI)