A Framework to Determine Active Connectivity within the Mouse Brain

Tremendous effort has focused on determining the physical connectivity within the mouse brain. However, the strength of connections within the brain constantly changes throughout the 24-hour day. Here, we combine experimental and computational methods to determine an "active connectivity" of the physical connections between the most active neurons. Brain cells of freely behaving mice are genetically marked with the activitydependent TRAP2 system, imaged, digitized, and their connectivity is inferred from the latest brain atlases. We apply our methods to determine the most active networks in the early light and early dark hours of the day, two periods with distinct differences in sleep, wake, and feeding behavior. Increased signaling is seen through the visceral and agranular insular (AI) regions in the early day as peripheral stimuli are integrated. On the other hand, there is an increase in the activity of the retrosplenial cortex (RSP) and the anterior cingulate cortex (ACC) during the early night, when more sustained attention is required. Our framework carves a window to the three-dimensional networks of active connections in the mouse brain that underlie spontaneous behaviors or responses to environmental changes, thus providing the basis for direct computer simulations and analysis of such networks in the future. ### Competing Interest Statement I have read the journal's policy and the authors of this manuscript have the following competing interests: H.R.U. is a co-inventor on patent applications covering the CUBIC reagents and a co-founder of CUBICStars Inc.