DiLFM: an artifact-suppressed and noise-robust light-field microscopy through dictionary learning

Yuanlong Zhang; Bo Xiong; Yi Zhang; Zhi Lu; Jiamin Wu; Qionghai Dai

doi:10.1038/s41377-021-00587-6

DiLFM: an artifact-suppressed and noise-robust light-field microscopy through dictionary learning

Light Sci Appl. 2021 Jul 27;10(1):152. doi: 10.1038/s41377-021-00587-6.

Authors

Yuanlong Zhang^#^{1

2

3}, Bo Xiong^#^{1

2

3}, Yi Zhang^{1

2

3}, Zhi Lu^{1

2

3}, Jiamin Wu^{4

5

6}, Qionghai Dai^{7

8

9}

Affiliations

¹ Department of Automation, Tsinghua University, Beijing, 100084, China.
² Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
³ Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China.
⁴ Department of Automation, Tsinghua University, Beijing, 100084, China. wujiamin@tsinghua.edu.cn.
⁵ Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China. wujiamin@tsinghua.edu.cn.
⁶ Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China. wujiamin@tsinghua.edu.cn.
⁷ Department of Automation, Tsinghua University, Beijing, 100084, China. qhdai@mail.tsinghua.edu.cn.
⁸ Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China. qhdai@mail.tsinghua.edu.cn.
⁹ Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China. qhdai@mail.tsinghua.edu.cn.

^# Contributed equally.

Abstract

Light field microscopy (LFM) has been widely used for recording 3D biological dynamics at camera frame rate. However, LFM suffers from artifact contaminations due to the illness of the reconstruction problem via naïve Richardson-Lucy (RL) deconvolution. Moreover, the performance of LFM significantly dropped in low-light conditions due to the absence of sample priors. In this paper, we thoroughly analyze different kinds of artifacts and present a new LFM technique termed dictionary LFM (DiLFM) that substantially suppresses various kinds of reconstruction artifacts and improves the noise robustness with an over-complete dictionary. We demonstrate artifact-suppressed reconstructions in scattering samples such as Drosophila embryos and brains. Furthermore, we show our DiLFM can achieve robust blood cell counting in noisy conditions by imaging blood cell dynamic at 100 Hz and unveil more neurons in whole-brain calcium recording of zebrafish with low illumination power in vivo.

Abstract

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