Biology subjects

SHE, Z.

Publications and source records attributed to SHE, Z..

4 recordsLinked to original sources

bioRxiv2026

Optical Windows for Transcranial Brain Imaging in Living Mice: Skull Thinning, Clearing, and Beyond

Longitudinal, noninvasive in vivo imaging is essential for studying brain physiology and pathological mechanisms. Advances in transcranial optical windows, including thinned-skull and optical clearing techniques, have markedly improved imaging depth and resolution when combined with multiphoton microscopy. However, their optical performance often deteriorates rapidly, and quantitative studies on long-term stability and the causes of image quality loss remain limited. In this work, we systematically investigated current transcranial window approaches using multiphoton excited fluorescence microscopy (MPEFM) and adaptive optics, examining longevity, optical aberrations, and imaging resolution. Our results reveal that progressive skull regrowth is a fundamental limitation across all window types, leading to substantial declines in signal quality and resolution for conventional MPEFM thereby reducing achievable high-resolution imaging depth. To address these challenges, we developed a localized glucocorticoid (GC) delivery strategy that significantly extends window performance for up to one month. Furthermore, we demonstrated that a GC-loaded hydrogel sealing method effectively suppressed skull regrowth while preserving optimal optical properties, offering a potential and practical route to chronic, high-fidelity transcranial imaging. These findings provide mechanistic insight into window degradation and establish a framework for sustained, long-term in vivo brain imaging.

neuroscience↗

bioRxiv2025

Toward Crosstalk-free All-optical Interrogation of Neural Circuits

All-optical interrogation, based on high-resolution two-photon stimulation and imaging, has emerged as a potentially transformative approach in neuroscience, allowing for the simultaneous precise manipulation and monitoring of neuronal activity across various model organisms. However, the unintended excitation of light-gated ion channels such as channelrhodopsin (ChR) during two-photon calcium imaging with genetically encoded calcium indicators (GECIs) introduces artifactual neuronal perturbation and contaminates neural activity measurements. In this study, we propose an active pixel power control (APPC) approach, which dynamically adjusts the imaging laser power at each scanning pixel, to address the challenge. We aim to achieve simultaneous two-photon optogenetic manipulation and calcium imaging with a single femtosecond laser, while minimizing the crosstalk between manipulation and imaging. To study this technologys capabilities, we applied it to the larval zebrafish brain in vivo. Our results demonstrate that the APPC approach preserves GECI signal quality while suppressing optogenetic artifacts significantly. This enhances the accuracy of neural circuit dissection and advances the precision of all-optical interrogation, offering a robust framework for probing neural circuit dynamics and causality in vivo with high fidelity, potentially across various model organisms. Importantly, this technology can be seamlessly integrated with commonly used two-photon microscope systems in laboratories worldwide.

neuroscience↗

bioRxiv2025

Rapid adaptive optics enabling near noninvasive high-resolution brain imaging in awake behaving mice

High-resolution imaging under physiological conditions is essential for studying biological mechanisms and disease processes. However, achieving this goal remains challenging due to optical aberrations and scattering from heterogeneous tissue structures, compounded by motion artifacts from awake animals. In this study, we developed a rapid and accurate adaptive optics system called multiplexing digital focus sensing and shaping (MD-FSS) for deep-tissue multiphoton microscopy. Under two-photon excitation, MD-FSS precisely measures the aberrated point spread function in approximately 0.1 s per measurement, effectively compensating for both aberrations and scattering to achieve subcellular resolution in deep tissue. Using MD-FSS integrated with two-photon microscopy, we achieved high-resolution brain imaging through thinned or optically cleared skull windows, two near noninvasive methods to access mouse brain, reaching depths up to 600 m below the pia in awake behaving mice. Our findings revealed significant differences in microglial functional states and microvascular circulation dynamics between awake and anesthetized conditions, highlighting the importance of studying brain function in awake mice through noninvasive methods. We captured functional imaging of fine neuronal structures at subcellular level in both somatosensory and visual cortices. Additionally, we demonstrated high-resolution imaging of microvascular structures and neurovascular coupling across multiple cortical regions and depths in the awake brain. Our work shows that MD-FSS robustly corrects tissue-induced aberrations and scattering through rapid PSF measurements, enabling near-noninvasive, high-resolution imaging in awake, behaving mice.

bioengineering↗

bioRxiv2021

Direct focus sensing and shaping for high-resolution multi-photon imaging in deep tissue

High-resolution optical imaging of deep tissue in-situ such as the living brain is fundamentally challenging because of the aberration and scattering of light. In this work, we develop an innovative adaptive optics three-photon microscope based on direct focus sensing and shaping that can accurately measure and effectively compensate for both low- and high-order specimen-induced aberrations and recover near-diffraction-limited performance at depth. A conjugate adaptive optics configuration with remote focusing enables in vivo imaging of fine neuronal structures in the mouse cortex through the intact skull up to a depth of 750 {micro}m below pia, making high-resolution microscopy in cortex near non-invasive. Functional calcium imaging with high sensitivity and accuracy, and high-precision laser-mediated microsurgery through the intact skull were demonstrated. Moreover, we also achieved in vivo high-resolution imaging of the deep cortex and subcortical hippocampus up to 1.1 mm below pia within the intact brain.

bioengineering↗