Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning

Zhaoqiang Wang; Lanxin Zhu; Hao Zhang; Guo Li; Chengqiang Yi; Yi Li; Yicong Yang; Yichen Ding; Mei Zhen; Shangbang Gao; Tzung K Hsiai; Peng Fei

doi:10.1038/s41592-021-01058-x

Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning

Nat Methods. 2021 May;18(5):551-556. doi: 10.1038/s41592-021-01058-x. Epub 2021 Feb 11.

Authors

Zhaoqiang Wang^#^{1

2

3}, Lanxin Zhu^#¹, Hao Zhang^#¹, Guo Li¹, Chengqiang Yi¹, Yi Li^{1

4}, Yicong Yang¹, Yichen Ding³, Mei Zhen⁵, Shangbang Gao⁶, Tzung K Hsiai^{7

8

9}, Peng Fei¹⁰

Affiliations

¹ School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.
² Department of Bioengineering, Henry Samueli School of Engineering and Applied Science, University of California, Los Angeles, Los Angeles, CA, USA.
³ Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
⁴ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
⁵ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.
⁶ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. sgao@hust.edu.cn.
⁷ Department of Bioengineering, Henry Samueli School of Engineering and Applied Science, University of California, Los Angeles, Los Angeles, CA, USA. THsiai@mednet.ucla.edu.
⁸ Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. THsiai@mednet.ucla.edu.
⁹ Division of Cardiology, Department of Medicine, Greater Los Angeles VA Healthcare System, Los Angeles, CA, USA. THsiai@mednet.ucla.edu.
¹⁰ School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China. feipeng@hust.edu.cn.

^# Contributed equally.

Abstract

Light-field microscopy has emerged as a technique of choice for high-speed volumetric imaging of fast biological processes. However, artifacts, nonuniform resolution and a slow reconstruction speed have limited its full capabilities for in toto extraction of dynamic spatiotemporal patterns in samples. Here, we combined a view-channel-depth (VCD) neural network with light-field microscopy to mitigate these limitations, yielding artifact-free three-dimensional image sequences with uniform spatial resolution and high-video-rate reconstruction throughput. We imaged neuronal activities across moving Caenorhabditis elegans and blood flow in a beating zebrafish heart at single-cell resolution with volumetric imaging rates up to 200 Hz.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Behavior, Animal
Biomechanical Phenomena
Caenorhabditis elegans / physiology*
Deep Learning*
Heart / physiology*
Image Processing, Computer-Assisted / methods*
Microscopy / methods*
Motor Activity / physiology
Neurons / physiology
Zebrafish

Abstract

Publication types

MeSH terms

Grants and funding