Yide Zhang

Yide Zhang

Incoming Assistant Professor of ECEE and BME

University of Colorado Boulder

Biography

My name is Yide Zhang (Chinese: 张以德). My long-term research goal is to pioneer optical imaging technologies that surpass current limits in speed, accuracy, and accessibility, advancing translational research. With a foundation in electrical engineering, particularly in biomedical imaging and optics, my PhD work at the University of Notre Dame focused on advancing multiphoton fluorescence lifetime imaging microscopy and super-resolution microscopy, significantly reducing image generation time and cost. I developed an analog signal processing method that enables real-time streaming of fluorescence intensity and lifetime data, and created the first Poisson-Gaussian denoising dataset to benchmark image denoising algorithms for high-quality, real-time applications in biomedical research. As a postdoc at the California Institute of Technology (Caltech), my research expanded to include pioneering photoacoustic imaging techniques, enabling noninvasive and rapid imaging of hemodynamics in humans. In the realm of quantum imaging, I developed innovative techniques utilizing spatial and polarization entangled photon pairs, overcoming challenges such as poor signal-to-noise ratios and low resolvable pixel counts. Additionally, I advanced ultrafast imaging methods for visualizing passive current flows in myelinated axons and electromagnetic pulses in dielectrics. My research is currently funded by the National Institutes of Health (NIH) K99/R00 Pathway to Independence Award.

I will join the University of Colorado Boulder (CU Boulder) as an Assistant Professor of Electrical, Computer & Energy Engineering (ECEE) and Biomedical Engineering (BME) in May 2025. My lab will be actively recruiting postdocs, graduate students, and CU Boulder undergraduates. We welcome applicants with backgrounds in electrical engineering, biomedical engineering, physics, computer science, mechanical engineering, optics, ultrasonics, imaging, or related fields. If you are interested, please send your CV to yide.zhang@colorado.edu.

Interests

  • Photoacoustic Imaging
  • Quantum Imaging
  • Ultrafast Imaging
  • Fluorescence Imaging
  • Machine Learning

Education

  • Ph.D. in Electrical Engineering, 2019

    University of Notre Dame

  • M.S. in Electrical Engineering, 2017

    University of Notre Dame

  • B.Eng. in Automation, 2014

    Huazhong University of Science and Technology

Experience

 
 
 
 
 

Assistant Professor of ECEE and BME

University of Colorado Boulder (CU Boulder)

May 2025 – Present Boulder, Colorado USA
 
 
 
 
 

NIH K99/R00 Postdoctoral Fellow

California Institute of Technology (Caltech)

Sep 2019 – Apr 2025 Pasadena, California USA

Journal Publications

(2024). Enhancing optical microscopy with quantum entanglement. Optics and Photonics News, vol. 35, no. 11, pp. 32-39.

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(2024). Sharp-peaked lanthanide nanocrystals for near-infrared photoacoustic multiplexed differential imaging. Communications Materials, vol. 5, no. 164, pp. 1-10.

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(2024). Quantum imaging of biological organisms through spatial and polarization entanglement. Science Advances, vol. 10, no. 10, pp. eadk1495.

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(2024). Editorial: Phasor analysis for fluorescence lifetime data. Frontiers in Bioinformatics (Editorial), vol. 4, no. 1375480, pp. 1-2.

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(2023). Deep learning-enhanced microscopy with extended depth-of-field. Light: Science & Applications (News & Views), vol. 12, no. 284, pp. 1-3.

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(2023). Quantum microscopy of cells at the Heisenberg limit. Nature Communications, vol. 14, no. 2441, pp. 1-8.

PDF DOI Caltech’s 2023 Year in Review Featured News

(2023). Experimental full-domain mapping of quantum correlation in Clauser-Horne-Shimony-Holt scenarios. Physical Review Applied, vol. 19, no. 034049, pp. 1-16.

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(2023). Single-pulse real-time billion-frames-per-second planar imaging of ultrafast nanoparticle-laser dynamics and temperature in flames. Light: Science & Applications, vol. 12, no. 47, pp. 1-12.

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(2023). High-gain and high-speed wavefront shaping through scattering media. Nature Photonics, vol. 17, no. 2, pp. 1-9.

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(2023). Non-invasive photoacoustic computed tomography of rat heart anatomy and function. Light: Science & Applications, vol. 12, no. 12, pp. 1-9.

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(2022). Optical-resolution photoacoustic microscopy with a needle-shaped beam. Nature Photonics, vol. 17, no. 1, pp. 89-95.

PDF DOI Nature Research Highlight Featured News

(2022). Label-free intraoperative histology of bone tissue via deep-learning-assisted ultraviolet photoacoustic microscopy. Nature Biomedical Engineering, vol. 6, no. 9, pp. 1-11.

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(2022). Ultrafast and hypersensitive phase imaging of propagating internodal current flows in myelinated axons and electromagnetic pulses in dielectrics. Nature Communications, vol. 13, no. 5247, pp. 1-12.

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(2022). Real-time image denoising of mixed Poisson–Gaussian noise in fluorescence microscopy images using ImageJ. Optica, vol. 9, no. 4, pp. 335-345.

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(2021). Instant FLIM enables 4D in vivo lifetime imaging of intact and injured zebrafish and mouse brains. Optica, vol. 8, no. 6, pp. 885-897.

PDF DOI Optica Top Downloads Control Software Analysis Software

(2020). Machine learning for faster and smarter fluorescence lifetime imaging microscopy. Journal of Physics: Photonics, vol. 2, no. 4, pp. 042005.

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(2020). Memory analysis for memristors and memristive recurrent neural networks. IEEE/CAA Journal of Automatica Sinica, vol. 7, no. 1, pp. 96-105.

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(2020). Resolution enhancement of transmission electron microscopy by super-resolution radial fluctuations. Applied Physics Letters, vol. 116, no. 4, pp. 044105.

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(2019). Automatic segmentation of intravital fluorescence microscopy images by K-means clustering of FLIM phasors. Optics Letters, vol. 44, no. 16, pp. 3928-3931.

PDF Code DOI Optics Letters’ Featured Paper of Volume 44, Issue 16

(2019). Generating intravital super-resolution movies with conventional microscopy reveals actin dynamics that construct pioneer axons. Development, vol. 146, no. 5, pp. dev171512.

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(2018). Generalized stepwise optical saturation enables super-resolution fluorescence lifetime imaging microscopy. Biomedical Optics Express, vol. 9, no. 9, pp. 4077-4093.

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(2018). Super-resolution fluorescence microscopy by stepwise optical saturation. Biomedical Optics Express, vol. 9, no. 4, pp. 1613-1629.

PDF Code DOI NDIIF Award for Best Biological Imaging Publication 2018 Featured News

(2017). Description of deep saturated excitation multiphoton microscopy for super-resolution imaging. Journal of the Optical Society of America A, vol. 34, no. 7, pp. 1217-1223.

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(2017). Silica-coated ruthenium-complex nanoprobes for two-photon oxygen microscopy in biological media. Optical Materials Express, vol. 7, no. 3, pp. 1066-1076.

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(2017). Saturation-compensated measurements for fluorescence lifetime imaging microscopy. Optics Letters, vol. 42, no. 1, pp. 155-158.

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(2016). Super-sensitivity multiphoton frequency-domain fluorescence lifetime imaging microscopy. Optics Express, vol. 24, no. 18, pp. 20862-20867.

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(2016). Investigation of signal-to-noise ratio in frequency-domain multiphoton fluorescence lifetime imaging microscopy. Journal of the Optical Society of America A, vol. 33, no. 7, pp. B1-B11.

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(2014). Exponential adaptive lag synchronization of memristive neural networks via fuzzy method and applications in pseudo random number generators. IEEE Transactions on Fuzzy Systems, vol. 22, no. 6, pp. 1704-1713.

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Selected Conference Publications

(2024). Ultrafast single-shot 3D photoacoustic tomography in vivo using a single-element detector. SPIE Photonics West 2024, San Francisco, California USA.

PDF DOI Seno Medical Best Paper Award

(2023). Ultrafast phase imaging of propagating current flows in myelinated axons and electromagnetic pulses in dielectrics. SPIE Photonics West 2023, San Francisco, California USA.

PDF DOI Hitachi High-Tech Best Presentation Award

(2019). A Poisson-Gaussian denoising dataset with real fluorescence microscopy images. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR 2019), Long Beach, California USA.

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(2019). Three-dimensional deep tissue multiphoton frequency-domain fluorescence lifetime imaging microscopy via phase multiplexing and adaptive optics. SPIE Photonics West 2019, San Francisco, California USA.

PDF DOI JenLab Young Investigator Award Video 1 Video 2 Featured News

Talks

Ultrafast single-shot 3D photoacoustic tomography in vivo using a single-element detector

We present photoacoustic computed tomography through an ergodic relay (PACTER), a method for single-shot 3D imaging of hemodynamics …

Ultrafast phase imaging of propagating current flows in myelinated axons and electromagnetic pulses in dielectrics

Visualization of the spatiotemporal dynamics of propagation is fundamental to understanding dynamic processes ranging from action …

Super-resolution multiphoton frequency-domain fluorescence lifetime imaging microscopy by generalized stepwise optical saturation (GSOS)

We present the first experimental demonstration of super-resolution multiphoton frequency-domain (FD) fluorescence lifetime imaging …

Posts

Single-shot 3D photoacoustic tomography based on a single-element detector for ultrafast imaging of hemodynamics

Single-shot 3D photoacoustic tomography based on a single-element detector for ultrafast imaging of hemodynamics

Single-laser-pulse photoacoustic tomography with a single-element ultrasonic transducer, equivalent to thousands of virtual detectors, allows for ultrafast (up to 1 kHz) volumetric imaging of hemodynamics in humans.

Upgrade a 2-photon microscope with high-speed FLIM for $2352

Upgrade a 2-photon microscope with high-speed FLIM for $2352

Lab On The Cheap is dedicated to sharing cheap alternatives to normally expensive lab equipment for all of us who would like to participate in the scientific revolution but don’t have the sponsorship to do so.

“Publish or perish” will not perish

“Publish or perish” will not perish

“Publish or perish”, as a widely accepted academic evaluation system, should not be discarded just because of its potential drawbacks.

Overview of my PhD projects

Overview of my PhD projects

Projects I completed during my PhD at the University Notre Dame

Software

Analysis software for instant FLIM

Instant FLIM enables 4D in vivo lifetime imaging of intact brains

Control software for instant FLIM

Instant FLIM enables 4D in vivo lifetime imaging of intact brains

K-means clustering of FLIM phasor

Automatic segmentation of intravital fluorescence microscopy images by K-means clustering of FLIM phasors

Fluorescence Microscopy Denoising (FMD) dataset

A Poisson-Gaussian denoising dataset with real fluorescence microscopy images

Deconvolution stepwise optical saturation (DeSOS) microscopy

Generating intravital super-resolution movies with conventional microscopy reveals actin dynamics that construct pioneer axons

Stepwise optical saturation (SOS) microscopy

Super-resolution fluorescence microscopy by stepwise optical saturation

Saturation-compensated FLIM

Saturation-compensated measurements for fluorescence lifetime imaging microscopy

SNR of MPM-FD-FLIM

Investigation of signal-to-noise ratio in frequency-domain multiphoton fluorescence lifetime imaging microscopy

Contact