Visual Cortex Circuitry and Arousal
Characterizing state-dependent organization of microscale functional circuitry in visual cortex using calcium imaging and Neuropixels
Brain state modulates sensory processing across visual cortex, yet how it relates to the organization of functional circuitry at the level of individual neurons and cell types remains largely unknown.
The data. We construct one of the largest microscale directed functional circuit maps in mouse visual cortex — calcium imaging of more than 57,000 neurons across four visual areas and five cortical layers.
Our approach. Using a time-aware causal inference framework, we map multi-scale organization of directed functional circuitry across arousal states. Key findings include:
- Laminar organization: layer 6 recurrence dominates within-layer; dominant between-layer pathways shift with arousal state (layer 5-to-6 in low arousal, layer 4-to-5 in high arousal)
- Cell-type specificity: spatial extent is selectively greater for excitatory-to-inhibitory connections in high arousal
- Structure-function coupling: across 6,597 electron-microscopy reconstructions of neuron pairs, synapse count predicts functional connection strength, with weaker coupling in high arousal
- Stimulus-driven prediction: neuron pairs with stronger functional connections show more similar predictive performance, varying by layer and cell type
Context. This project is embedded within the broader research program of the Abbasi-Asl Lab at UCSF, which investigates interpretable machine learning approaches to understanding neural computation in sensory cortices.