Longitudinal tracking of neuronal activity from the same cells in the developing brain using Track2p

Understanding cortical circuit development requires tracking neuronal activity across days in the growing brain. While in vivo calcium imaging now enables such longitudinal studies, automated tools for reliably tracking large populations of neurons across sessions remain limited. Here, we present a novel cell tracking method based on sequential image registration, validated on calcium imaging data from the barrel cortex of mouse pups over 1 postnatal week. Our approach enables robust long-term analysis of several hundreds of individual neurons, allowing quantification of neuronal dynamics and representational stability over time. Using this method, we identified a key developmental transition in neuronal activity statistics, marking the emergence of arousal state modulation. Beyond this key finding, our method provides an essential tool for tracking developmental trajectories of individual neurons, which could help identify potential deviations associated with neurodevelopmental disorders.