Yide Zhang

Yide Zhang

Postdoctoral Scholar

California Institute of Technology

Biography

I am a postdoctoral scholar 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. My research interests include photoacoustic microscopy, photoacoustic computed tomography, compressed ultrafast photography, nonlinear microscopy, multiphoton microscopy, fluorescence lifetime imaging microscopy, super-resolution microscopy, high-speed imaging, deep tissue imaging, adaptive optics, computational imaging, deep learning.

Interests

  • Photoacoustic tomography
  • Compressed ultrafast photography
  • Multiphoton microscopy
  • Fluorescence lifetime imaging microscopy
  • Super-resolution microscopy
  • 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

 
 
 
 
 

Postdoctoral Scholar

Caltech Optical Imaging Laboratory

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

Research Assistant

Biophotonics Research Group

Aug 2014 – Sep 2019 Notre Dame, Indiana USA
Development of novel 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

Overview of my PhD projects

Overview of my PhD projects

Projects I completed during my PhD at the University Notre Dame

“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.

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

(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 Control Software Analysis Software

(2021). Snapshot photoacoustic topography through an ergodic relay of optical absorption in vivo. Nature Protocols, vol. 16, no. 5, pp. 2381-2394.

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(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

(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.

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

Code DOI 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

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

Code DOI

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

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

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(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 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.

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(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.

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(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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