Ph.D Thesis

Ph.D StudentMcley Liron
SubjectFunctional Optoacoustic Neuro-Tomography in the Mouse
Brain In Vivo
DepartmentDepartment of Biomedical Engineering
Supervisors PROFESSOR EMERITUS Eitan Kimmel
PROF. Shy Shoham


The visualization of neural activity across multiple brain areas at a high spatiotemporal resolution can greatly contribute to our understanding of brain function. Optical imaging methods enable an excellent spatiotemporal resolution and informative contrasts but their penetration depths are limited, while functional ultrasound and MRI, have excellent penetration but their contrast relates indirectly to neural activity. Optoacoustic imaging has the potential to address this tradeoff by combining optical contrast and acoustic readout, which has the benefit of weak scattering in biological tissue. Optoacoustic tomography-based methods have also demonstrated image reconstruction capabilities of large fields of view at a high temporal rate.

This study builds upon our team’s recent collaborative work that showed that calcium indicators have an optoacoustic signature and introduced functional optoacoustic neuro-tomography (FONT), demonstrating its use for calcium optoacoustic imaging in larva and adult zebrafish in vivo. The goal of this research was to extend these results to the mouse model in vivo and establish FONT as a viable neuro-investigation tool.

To address this challenge we developed a FONT system capable of imaging the mouse brain during visual stimulation, and combined it with two complementary wide-field fluorescence imaging paradigms, enabling either consecutive or simultaneous OA and fluorescence imaging. We then used the system to observe brain activity in several transgenic mouse lines expressing GCaMP6-type genetically encoded calcium indicators throughout the cortex and other brain areas. Using our imaging results and a new analysis pipeline, we robustly identified, characterized and decoupled the fluorescence signatures of visually-evoked and characteristic spontaneous neural events, and explored the functional optoacoustic signature of these responses.

This work is an important step in the advancement of optoacoustic tomography as a diverse tool for investigating neural circuit dynamics in the intact mammalian brain.