Protocol for identifying and comparing neuronal ensembles using different algorithms within a graphical user interface

Neuronal ensembles are groups of neurons with coordinated activity that are related to a specific brain function. Here, we present a protocol to identify and compare neuronal ensembles from neuronal activity data obtained through two-photon microscopy or electrophysiological recordings using a unified graphical user interface (Ensembles Comparison and Recognition [ENCORE]). We describe steps for installing ENCORE, data loading, neuronal ensemble identification, inspecting results, and comparison of five different algorithms. We then detail procedures for evaluating functional relevance of identified neuronal ensembles. For complete details on the use and execution of this protocol, please refer to Carrillo-Reid.¹.