Simultaneous single-cell calcium imaging of neuronal population activity and brain-wide BOLD fMRI

Functional magnetic resonance imaging (fMRI) based on the blood-oxygen-level-dependent (BOLD) signal is widely used to study brain activity non-invasively. However, the relationship between the local neural population activity and vascular activity, as measured by BOLD fMRI, remains incompletely understood. Here we show that simultaneous measurement of cellular calcium (Ca²⁺) activity and whole-brain BOLD fMRI in awake mice can reveal spatially specific relationships between neurons and the surrounding vasculature. We introduce an MRI-compatible single-photon microscope that enables recordings from genetically defined neurons at cellular resolution during fMRI. Using this approach, we find that neurons located close to blood vessels often show a negative relationship with the local BOLD signal, whereas neurons farther away display a more variable, often positive relationship. We further demonstrate that local neural activity can be linked to BOLD responses across distributed, connected brain regions. Together, these results provide insight into how vascular organization shapes fMRI signals and establish a powerful tool for bridging cellular and whole-brain measurements of brain function.