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ProbeInterface: A Unified Framework for Probe Handling in Extracellular Electrophysiology

Abstract : Recording neuronal activity with penetrating extracellular multi-channel electrode arrays, more commonly known as neural probes, is one of the most widespread approaches to probe neuronal activity. Despite a plethora of available extracellular probe designs, the time-consuming process of mapping of electrode channel order and relative geometries, as required by spike-sorting software is invariably left to the end-user. Consequently, this manual process is prone to mis-mapping mistakes, which in turn lead to undesirable spike-sorting errors and inefficiencies. Here, we introduce ProbeInterface , an open-source project that aims to unify neural probe metadata descriptions by removing the manual step of probe mapping prior to spike-sorting for the analysis of extracellular neural recordings. ProbeInterface is first of all a Python API, which enables users to create and visualize probes and probe groups at any required complexity level. Second, ProbeInterface facilitates the generation of comprehensive wiring description in a reproducible fashion for any specific data-acquisition setup, which usually involves the use of a recording probe, a headstage, adapters, and an acquisition system. Third, we collaborate with probe manufacturers to compile an open library of available probes, which can be downloaded at run time using our Python API. Finally, with ProbeInterface we define a file format for probe handling which includes all necessary information for a FAIR probe description and is compatible with and complementary to other open standards in neuroscience.
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https://hal.archives-ouvertes.fr/hal-03576843
Contributor : Samuel Garcia Connect in order to contact the contributor
Submitted on : Wednesday, February 16, 2022 - 12:21:05 PM
Last modification on : Saturday, September 24, 2022 - 3:04:06 PM
Long-term archiving on: : Tuesday, May 17, 2022 - 6:34:44 PM

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Samuel Garcia, Julia Sprenger, Tahl Holtzman, Alessio P Buccino. ProbeInterface: A Unified Framework for Probe Handling in Extracellular Electrophysiology. Frontiers in Neuroinformatics, Frontiers, 2022, 16, pp.823056. ⟨10.3389/fninf.2022.823056⟩. ⟨hal-03576843⟩

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