A platform for brain-wide functional ultrasound imaging and analysis of circuit dynamics in behaving mice

Abstract

Imaging of large-scale circuit dynamics is crucial to gain a better understanding of brain function, but most techniques have a limited depth of field. Here we describe vfUSI, a platform for brain-wide volumetric functional ultrasound imaging of hemodynamic activity in awake head-fixed mice. We combined high-frequency 1024-channel 2D-array transducer with advanced multiplexing and highperformance computing for real-time 3D Power Doppler imaging at high spatiotemporal resolution (220x280x175-µm 3 voxel size, up to 6 Hz). In addition, we developed a standardized software pipeline for registration and segmentation based on the Allen Mouse Common Coordinate Framework, allowing for temporal analysis in 268 individual brain regions. We demonstrate the high sensitivity of vfUSI in multiple experimental situations where stimulus-evoked activity can be recorded using a minimal number of trials. We also mapped neural circuits in vivo across the whole brain during optogenetic activation of specific cell-types. Moreover, we revealed the sequential activation of sensory-motor regions during a grasping water droplet task. vfUSI will become a key neuroimaging technology because it combines ease of use, reliability, and affordability.

Chronic brain functional ultrasound imaging in freely moving rodents performing cognitive tasks

“…The capability to scan the brain and identify new regions will only improve as fUS technology improves. Volumetric fUS (Brunner et al, 2020; Rabut et al, 2019), for example will enable near full-brain imaging, and new signal processing for ultrasound (Bar-Zion et al, 2021) have the potential to vastly improve the speed and signal quality of fUS data reconstruction from the ultrasound returns. fUS can also be combined with optogenetics (Sans-Dublanc et al, 2021) so one can study the extent of the perturbations happening as it is increasingly acknowledged that even targeted brain perturbation has global effects (Lee et al, 2010).…”

“…8B). Additional assessment of D-V stability can be obtained by emerging volumetric fUS recordings (Brunner et al, 2020). These recordings will enable full 3D alignment of the brain between sessions.…”

Volumetric ultrasound localization microscopy of the whole brain microvasculature

“…The lower resolution we obtain compared to the 2D case is to be put in perspective as the frequency of the probe is different and the 4D ultrasound scanner is an innovative design and not a commercial one. Higher frequency fully populated 52 or sparse array probes are beginning to emerge as valid alternatives to fully addressed probes and we expect our technique to be translatable to any probe design 53,54 .…”

Volumetric ultrasound localization microscopy of the whole brain microvasculature

“…The lower resolution we obtain compared to the 2D case is to be put in perspective as the frequency of the probe is different and the 4D ultrasound scanner is an innovative design and not a commercial one. Higher frequency fully populated 48 or sparse array probes are beginning to emerge as valid alternatives to fully addressed probes and we expect our technique to be translatable to any probe design 49,50 .…”