A universal pipeline for the alignment of electrode tracks with slice histology and electrophysiological data

Abstract

Modern electrophysiological experiments in neuroscience typically measure the activity of hundreds of neurons across multiple brain regions. Each recorded neuron has to be assigned its correct area of origin, which can be estimated using histological reconstructions of electrode tracks. However, this approach has a limited accuracy with which the probe position can be determined. While some tools exist to assist in this process in mice, such tools are scarce for other species, such as rats or macaques. Moreover, even in mice, a more reliable brain area assignment may be achieved by using spiking response properties to delineate area boundaries along the recording probe. Here we present the Universal Probe Finder, which provides multi-species support for reconstructing a probes brain area per spike-sorted cluster or recording site. It can use various data formats and can calculate neuronal responsiveness to experimental interventions with only event times and spike times to provide further neurophysiological markers that simplify and improve the reliability of assigning brain areas to neurons. The program can be downloaded here: https://github.com/JorritMontijn/UniversalProbeFinder.