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https://github.com/SpikeInterface/spikeinterface
A Python-based module for creating flexible and robust spike sorting pipelines.
https://github.com/SpikeInterface/spikeinterface
electrophysiology neuroscience spike-sorting
Last synced: 3 months ago
JSON representation
A Python-based module for creating flexible and robust spike sorting pipelines.
- Host: GitHub
- URL: https://github.com/SpikeInterface/spikeinterface
- Owner: SpikeInterface
- License: mit
- Created: 2019-07-12T13:07:46.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2024-07-06T08:37:08.000Z (4 months ago)
- Last Synced: 2024-07-06T09:03:03.972Z (4 months ago)
- Topics: electrophysiology, neuroscience, spike-sorting
- Language: Python
- Homepage: https://spikeinterface.readthedocs.io
- Size: 62.4 MB
- Stars: 457
- Watchers: 25
- Forks: 178
- Open Issues: 229
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-neuroscience - SpikeInterface - Framework designed to unify spike-sorting technologies (Programming / Python)
README
# SpikeInterface: a unified framework for spike sorting
Latest Release
Documentation
License
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[](https://twitter.com/spikeinterface) [](https://fosstodon.org/@spikeinterface)
> :rocket::rocket::rocket:
> **New features!**: after months of development and testing, we are happy to announce that
> the latest release (0.101.0) includes a major API improvement: the `SortingAnalyzer`!
> To read more about why we did this, checkout the
> [SpikeInterface Enhancement Proposal](https://github.com/SpikeInterface/spikeinterface/issues/2282).
> Please follow this guide to transition from the old API to the new one:
> [Updating from legacy](https://spikeinterface.readthedocs.io/en/0.101.0/tutorials/waveform_extractor_to_sorting_analyzer.html).
SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.
Please [Star](https://github.com/SpikeInterface/spikeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/spikeinterface/subscription) to always stay up-to-date!
With SpikeInterface, users can:
- read/write many extracellular file formats.
- pre-process extracellular recordings.
- run many popular, semi-automatic spike sorters (also in Docker/Singularity containers).
- post-process sorted datasets.
- compare and benchmark spike sorting outputs.
- compute quality metrics to validate and curate spike sorting outputs.
- visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)
- export a report and/or export to phy
- offer a powerful Qt-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui)
- have powerful sorting components to build your own sorter.
## Documentation
Detailed documentation of the latest PyPI release of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/stable).
Detailed documentation of the development version of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/latest).
Several tutorials to get started can be found in [spiketutorials](https://github.com/SpikeInterface/spiketutorials).
Checkout our YouTube channel for video tutorials: [SpikeInterface YouTube Channel](https://www.youtube.com/@Spikeinterface).
There are also some useful notebooks [on our blog](https://spikeinterface.github.io) that cover advanced benchmarking
and sorting components.
You can also have a look at the [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui).
## How to install spikeinterface
You can install the latest version of `spikeinterface` version with pip (using quotes ensures `pip install` works in all terminals/shells):
```bash
pip install "spikeinterface[full]"
```
The `[full]` option installs all the extra dependencies for all the different sub-modules.
To install all interactive widget backends, you can use:
```bash
pip install "spikeinterface[full,widgets]"
```
To get the latest updates, you can install `spikeinterface` from source:
```bash
git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
pip install -e .
cd ..
```
## Citation
If you find SpikeInterface useful in your research, please cite:
```bibtex
@article{buccino2020spikeinterface,
title={SpikeInterface, a unified framework for spike sorting},
author={Buccino, Alessio Paolo and Hurwitz, Cole Lincoln and Garcia, Samuel and Magland, Jeremy and Siegle, Joshua H and Hurwitz, Roger and Hennig, Matthias H},
journal={Elife},
volume={9},
pages={e61834},
year={2020},
publisher={eLife Sciences Publications Limited}
}
```
Please also cite other relevant papers for the specific components you use.
For a ful list of references, please check the [references](https://spikeinterface.readthedocs.io/en/latest/references.html) page.