Metadata-Version: 2.1
Name: probeinterface
Version: 0.2.17
Summary: Python package to handle probe layout, geometry and wiring to device.
Author-email: Samuel Garcia <sam.garcia.die@gmail.com>, Alessio Buccino <alessiop.buccino@gmail.com>
Project-URL: homepage, https://github.com/SpikeInterface/probeinterface
Project-URL: repository, https://github.com/SpikeInterface/probeinterface
Project-URL: documentation, https://probeinterface.readthedocs.io
Project-URL: changelog, https://probeinterface.readthedocs.io/en/main/release_notes.html
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Provides-Extra: docs
Requires-Dist: pillow ; extra == 'docs'
Requires-Dist: sphinx-gallery ; extra == 'docs'
Requires-Dist: matplotlib (>=3.2.2) ; extra == 'docs'
Requires-Dist: scipy ; extra == 'docs'
Requires-Dist: pandas ; extra == 'docs'
Provides-Extra: test
Requires-Dist: pytest ; extra == 'test'
Requires-Dist: matplotlib ; extra == 'test'
Requires-Dist: scipy ; extra == 'test'
Requires-Dist: pandas ; extra == 'test'
Requires-Dist: h5py ; extra == 'test'

# 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.

Documentation : https://probeinterface.readthedocs.io/


## Goals

Make a lightweight package to handle:

  * probe contact geometry (both 2D and 3D layouts)
  * probe shape (contour of the probe, shape of channel contact, ...)
  * probe wiring to device (the physical layout often doesn't match the channel ordering)
  * combining several probes into a device with global geometry + global wiring
  * exporting probe geometry data into JSON files
  * loading existing probe geometry files (Neuronexus, imec, Cambridge Neurotech...) [Started here](https://gin.g-node.org/spikeinterface/probeinterface_library)

Bonus :

  * optional plotting (based on `matplotlib`)
  * load/save geometry using common formats (PRB, CSV, NWB, ...)
  * handle SI length units correctly um/mm/...


Target users/projet :

  * spikeinterface team : integrate this into spikeextractor for channel location
  * neo team : handle array_annotations for AnalogSignal
  * spikeforest team : use this package for ploting probe activity
  * phy team: integrate for probe display
  * spyking-circus team : handle probe with this package
  * kilosort team : handle probe with this package
  * tridesclous team : handle probe with this package
  * open ephys team : automatically generate channel map configuration files


 Author: Samuel Garcia
