3D fluorescence and phase microscopy with scattering samples

Yi Xue

(UC Davis)

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Date: October 19, 2022


Optical imaging is often hindered by light scattering. Scattered photons contribute to the background noise and degrade the signal-to-noise ratio (SNR) of fluorescent images. To tackle this challenge, I developed several strategies for both multiphoton microscopy and one-photon microscopy to image through scattering media. Multiphoton microscopy has been widely used for deep tissue imaging due to long excitation wavelength and inherent optical sectioning ability, but imaging speed is relatively slow because of scanning. Multiphoton microscopy with parallelized excitation and detection improves the imaging speed, but scattered fluorescent photons degrade the SNR of images. To achieve both high speed and high SNR, I developed a two-photon imaging technique that combines structured illumination and a digital filter of spatial frequency to discard scattered photons and only keeps ballistic photons. On the other hand, scattered photons carry the information of the heterogeneity of scattering media, quantitatively evaluated by refractive index. Instead of discarding scattered photons, I developed a one-photon technique that decodes the refractive index of media from scattered fluorescence images. This technique models a scattering medium as a series of thin layers and describe the light path in the medium. By measuring the fluorescent images and solving the inverse problem, this technique enables the reconstruction of the 3D refractive index of scattering media and digital correction of scattering in fluorescence images.

Further Information:

Yi Xue is an assistant professor at the University of California, Davis. She received her PhD and MS degrees in Mechanical Engineering from Massachusetts Institute of Technology in 2019 and 2015, respectively, and her BEng degree in Optical Engineering from Zhejiang University, China, in 2013. She received JenLab Young Investigator Award and Weill Neurohub Fellowship. Her current research interests include computational optics, multiphoton microscopy, brain imaging and optogenetics.

Created: Monday, October 24th, 2022