Yide Zhang

Yide Zhang

NIH K99 Postdoctoral Fellow

California Institute of Technology

Biography

My name is Yide Zhang (Chinese: 张以德). I am an NIH K99 Postdoctoral Fellow at the Caltech Optical Imaging Laboratory, under the supervision of Prof. Lihong V. Wang. My research is interdisciplinary and focused on developing new types of optical imaging techniques that could advance the work of other researchers and medical personnel in a wide variety of fields. Currently, I am developing next-generation photoacoustic and ultrafast imaging techniques that can observe biological and physical phenomena that are too fast to be imaged with existing methods. The observation of the ultrafast phenomena could provide a better understanding of the fundamentals of life and physical sciences. I am also developing novel quantum imaging approaches that can investigate biological organisms with an imaging performance that cannot be achieved using classical optical imaging. In my free time, I enjoy cooking, hiking, cycling, and traveling.

Interests

  • Photoacoustic imaging
  • Ultrafast imaging
  • Quantum imaging
  • Fluorescence imaging
  • Brain imaging
  • Artificial intelligence in imaging

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

 
 
 
 
 

NIH K99 Postdoctoral Fellow

Caltech Optical Imaging Laboratory

Sep 2019 – Present Pasadena, California USA
Development of novel photoacoustic tomography (PAT), compressed ultrafast photography (CUP), and quantum imaging techniques.
 
 
 
 
 

Research Assistant

Biophotonics Research Group

Aug 2014 – Sep 2019 Notre Dame, Indiana USA
Development of novel two-photon fluorescence lifetime imaging microscopy (FLIM) and super-resolution microscopy techniques.
 
 
 
 
 

Research Assistant

National Key Laboratory of Image Processing & Intelligence

Aug 2014 – Sep 2019 Wuhan, Hubei China
Development of memristive neural networks for artificial intelligence.

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

Journal Publications

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

DOI Featured News

(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.

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.

DOI Light: Science & Applications Top Downloads Featured News

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

DOI Featured News

(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.

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.

DOI Featured News

(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.

DOI Featured News

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

DOI

(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.

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.

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.

Code Video DOI Featured News 1 Featured News 2

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

DOI

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

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.

Code DOI

(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.

Code DOI

(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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Conference Publications

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

DOI Seno Medical Best Paper Award

(2024). Quantum imaging of biological organisms using hyperentangled photon pairs. SPIE Photonics West 2024, San Francisco, California USA.

(2024). Super-resolution quantum microscopy at the Heisenberg limit. SPIE Photonics West 2024, San Francisco, California USA.

DOI

(2024). Experimental full-domain mapping of quantum correlation in Clauser-Horne-Shimony-Holt scenarios. SPIE Photonics West 2024, San Francisco, California USA.

DOI

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

DOI Hitachi High-Tech Best Presentation Award

(2023). Non-invasive photoacoustic computed tomography of cardiac anatomy and function in rats. SPIE Photonics West 2023, San Francisco, California USA.

DOI

(2023). Needle-shaped beam optical-resolution photoacoustic microscopy with an extended depth of field. SPIE Photonics West 2023, San Francisco, California USA.

DOI

(2022). Label-free ultraviolet photoacoustic histology via deep learning for rapid intraoperative diagnosis of bone cancer. SPIE Photonics West 2022, San Francisco, California USA.

Best Paper Award of Photons Plus Ultrasound Conference

(2021). Convolutional neural network denoising in fluorescence lifetime imaging microscopy (FLIM). SPIE Photonics West 2021, Online Only.

Code DOI BiOS’21 3-Minute Poster Prize

(2021). Deep learning-based super-resolution fluorescence microscopy on small datasets. SPIE Photonics West 2021, Online Only.

Code DOI

(2021). Overcoming the fundamental limitation of frequency-domain fluorescence lifetime imaging microscopy spatial resolution. SPIE Photonics West 2021, Online Only.

DOI

(2020). Instant image denoising plugin for ImageJ using convolutional neural networks. Biomedical Optics 2020, Washington, DC USA.

Code DOI

(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.

Code Dataset DOI

(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.

DOI JenLab Young Investigator Award Video 1 Video 2 Featured News

(2019). Super-resolution multiphoton frequency-domain fluorescence lifetime imaging microscopy by generalized stepwise optical saturation (GSOS). SPIE Photonics West 2019, San Francisco, California USA.

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(2019). Self-calibrated frequency domain diffuse optical spectroscopy with a phased source array. SPIE Photonics West 2019, San Francisco, California USA.

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(2018). Super-resolution and high-speed quantitative multiphoton microscopy. Seventh Annual Harper Cancer Research Institute Research Day, Notre Dame, Indiana USA.

DOI Poster Contest Third Prize

(2018). Stepwise optical saturation microscopy: obtaining super-resolution images with conventional fluorescence microscopes. Biomedical Optics 2018, Hollywood, Florida USA.

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(2017). Super-resolution fluorescence imaging by stepwise optical saturation microscopy. IEEE Annual Mini-symposium on Electron Devices and Photonics, Notre Dame, Indiana USA.

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(2017). Doubling the sensitivity of multiphoton frequency-domain fluorescence lifetime images. CLEO: Applications and Technology 2017, San Jose, California USA.

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(2017). Simulation and experimental design of saturated excitation (SAX) multiphoton microscopy (MPM). CLEO: Applications and Technology 2017, San Jose, California USA.

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(2017). Super-sensitivity and super-resolution multiphoton fluorescence lifetime imaging microscopy. NDnano Symposium: Nanotechnology in the Treatment of Neurodegenerative Disorders, Notre Dame, Indiana USA.

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(2016). Highly stable two-photon oxygen imaging probe based on a ruthenium-complex encapsulated in a silica-coated nanomicelle. CLEO: Applications and Technology 2016, San Jose, California USA.

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(2016). Theoretical analysis of the signal-to-noise ratio of two-photon oxygen imaging probes. Biomedical Optics 2016, Fort Lauderdale, Florida USA.

DOI

(2016). High-resolution frequency-domain multiphoton fluorescence lifetime imaging microscopy. Fifth Annual Harper Cancer Research Institute Research Day, Notre Dame, Indiana USA.

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(2015). On increasing the imaging rate of frequency-domain multiphoton fluorescence lifetime imaging microscopy. IEEE Annual Mini-symposium on Electronic and Photonics, Notre Dame, Indiana USA.

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(2014). Implementation of memristive neural networks with spike-rate-dependent plasticity synapse. IEEE International Joint Conference on Neural Networks (IJCNN), Beijing, China.

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