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.
Highlights
Recording neural signals from extracellular electrodes is one of the most widely used techniques to probe neural activity
We present ProbeInterface, a lightweight and userfriendly Python framework to standardize the description and handling of neural probe mapping for subsequent data analysis
After introducing the main concepts of the ProbeInterface framework (Figure 1), we demonstrate how the Python API can be used to create a probe configuration from scratch (Figure 2) and to retrieve a commercial probe from the ProbeInterface public library (Figure 3)
Summary
Recording neural signals from extracellular electrodes is one of the most widely used techniques to probe neural activity. It is in most cases left to the end user to correctly retrieve the mapping information for their probe from the vendor, to parse the geometric information into file formats that are specific to their chosen spike sorter (e.g., a .prb file for Klusta, Spyking CIRCUS, a .mat file for Kilosort and Ironclust, etc.), and to properly verify that the wiring between each recording electrode and the acquired signal is consistent and correct This last step can be quite tedious and error-prone as most probes require connection to the data-acquisition system via headstages and / or adapters which result in a re-ordering of the signals. ProbeInterface comes with a JSON-based file format that carries all relevant metadata about the probe, including the geometry of the electrode (position, shape, size), the intrinsic channel indices, the size of the silicon shanks, and more
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