Python package to handle probe layout, geometry and wiring to device.
Project description
probeinterface
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A Python package to handle the layout, geometry, and wiring of silicon probes for extracellular electrophysiology experiments.
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Goals
ProbeInterface aims to provide a common framework to handle probe information across neuroscience experiments.
ProbeInterface is used by the SpikeInterface package to attach probe information to a recording object. You can find detailed documentation in the SpikeInterface documentation.
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
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.
Detailed documentation of the development version of ProbeInterface can be found here.
How to install probeinterface
You can install the latest version of probeinterface version with pip:
pip install probeinterface
To get the latest updates, you can install probeinterface from source:
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:
@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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