NeuroCarto: A Toolkit for Building Custom Read-out Channel Maps for High Electrode-count Neural Probes

Neuropixels probes contain thousands of electrodes across one or more shanks and are sufficiently small to allow chronic recording of neural activity in freely behaving small animals. However, the joint increase in the number of electrodes and miniaturization of the probe package has led to a compromise in which groups of electrodes share a single read-out channel and only a fraction of the electrodes can be read out at any given time. Experimenters then face the challenge of selecting a subset of electrodes (i.e., channel map) that both covers the brain regions of interest and adheres to the restrictions of the underlying hardware. Here, we present NeuroCarto, a Python toolkit and GUI to simplify the construction of a custom channel map for Neuropixels probes. We describe a general iterative approach to select electrodes and provide a specific implementation that allows experimenters to specify a blueprint of regions of interest along the probe shanks and the desired local electrode density. NeuroCarto assists in generating a channel map from the blueprint and visualizes potential read-out channel conflicts. We showcase the utility of NeuroCarto in an experimental workflow to simultaneously record from the dorsal and ventral hippocampus with 4-shank Neuropixels 2.0 probes in freely moving mice.