| Name | probeinterface JSON |
| Version |
0.2.21
JSON |
| download |
| home_page | |
| Summary | Python package to handle probe layout, geometry and wiring to device. |
| upload_time | 2024-02-05 10:35:52 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
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# probeinterface
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/probeinterface/">
<img src="https://img.shields.io/pypi/v/probeinterface.svg" alt="latest release" />
</a>
</td>
</tr>
<tr>
<td>Documentation</td>
<td>
<a href="https://probeinterface.readthedocs.io/">
<img src="https://readthedocs.org/projects/probeinterface/badge/?version=latest" alt="latest documentation" />
</a>
</td>
</tr>
<tr>
<td>License</td>
<td>
<a href="https://github.com/probeinterface/probeinterface/blob/main/LICENSE">
<img src="https://img.shields.io/pypi/l/probeinterface.svg" alt="license" />
</a>
</td>
</tr>
<tr>
<td>Build Status</td>
<td>
<a href="https://github.com/SpikeInterface/probeinterface/actions/workflows/full_tests.yml/badge.svg">
<img src="https://github.com/SpikeInterface/probeinterface/actions/workflows/full_tests.yml/badge.svg" alt="CI build status" />
</a>
</td>
</tr>
<tr>
<td>Codecov</td>
<td>
<a href="https://codecov.io/github/SpikeInterface/probeinterface">
<img src="https://codecov.io/gh/SpikeInterface/probeinterface/branch/main/graphs/badge.svg" alt="codecov" />
</a>
</td>
</tr>
</table>
A Python package to handle the layout, geometry, and wiring of silicon probes for extracellular electrophysiology experiments.
Please [Star](https://github.com/SpikeInterface/probeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/probeinterface/subscription) to always stay up-to-date!
## Goals
ProbeInterface aims to provide a common framework to handle probe information across neuroscience experiments.
ProbeInterface is used by the [SpikeInterface](https://github.com/SpikeInterface/spikeinterface) package to attach probe information to a recording object.
You can find detailed documentation in the [SpikeInterface documentation](https://spikeinterface.readthedocs.io/en/latest/modules/core.html#handling-probes).
In practice, ProbeInterface is a lightweight package to handle:
* probe contact geometry (both 2D and 3D layouts)
* probe shape (contour of the probe, shape of channel contacts, etc.)
* probe wiring to a device (the physical layout often doesn't match the channel ordering)
* combining several probes into a device, with probe groups and a global wiring
* exporting probe data into a common JSON file format
* loading existing probe geometry files (Cambridge Neurotech, NeuroNexus, etc.) from the [probeinterface_library](https://github.com/SpikeInterface/probeinterface_library)
In addition, ProbeInterface also offers the following features:
* `matplotlib`-based plotting functions
* loading/saving probes using common formats (PRB, CSV, NWB, ...)
* correctly handling SI units (um, mm)
## Documentation
Detailed documentation of the latest PyPI release of ProbeInterface can be found [here](https://probeinterface.readthedocs.io/en/0.2.18).
Detailed documentation of the development version of ProbeInterface can be found [here](https://probeinterface.readthedocs.io/en/latest).
## How to install probeinterface
You can install the latest version of `probeinterface` version with pip:
```bash
pip install probeinterface
```
To get the latest updates, you can install `probeinterface` from source:
```bash
git clone https://github.com/SpikeInterface/probeinterface.git
cd probeinterface
pip install -e .
cd ..
```
## Citation
If you find ProbeInterface useful in your research, please cite:
```bibtex
@article{garcia2022probeinterface,
title={ProbeInterface: a unified framework for probe handling in extracellular electrophysiology},
author={Garcia, Samuel and Sprenger, Julia and Holtzman, Tahl and Buccino, Alessio P},
journal={Frontiers in Neuroinformatics},
volume={16},
pages={823056},
year={2022},
publisher={Frontiers Media SA}
}
```
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