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3D localization for light-field microscopy via convolutional sparse coding on epipolar images

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Title: 3D localization for light-field microscopy via convolutional sparse coding on epipolar images
Authors: Song, P
Verinaz Jadan, H
Howe, C
Quicke, P
Foust, A
Dragotti, PL
Item Type: Journal Article
Abstract: Light-field microscopy (LFM) is a type of all-optical imaging system that is able to capture 4D geometric information of light rays and can reconstruct a 3D model from a single snapshot. In this paper, we propose a new 3D localization approach to effectively detect 3D positions of neuronal cells from a single light-field image with high accuracy and outstanding robustness to light scattering. This is achieved by constructing a depth-aware dictionary and by combining it with convolutional sparse coding. Specifically, our approach includes 3 key parts: light-field calibration, depth-aware dictionary construction, and localization based on convolutional sparse coding (CSC). In the first part, an observed raw light-field image is calibrated and then decoded into a two-plane parameterized 4D format which leads to the epi-polar plane image (EPI). The second part involves simulating a set of light-fields using a wave-optics forward model for a ball-shaped volume that is located at different depths. Then, a depth-aware dictionary is constructed where each element is a synthetic EPI associated to a specific depth. Finally, by taking full advantage of the sparsity prior and shift-invariance property of EPI, 3D localization is achieved via convolutional sparse coding on an observed EPI with respect to the depth-aware EPI dictionary. We evaluate our approach on both non-scattering specimen (fluorescent beads suspended in agarose gel) and scattering media (brain tissues of genetically encoded mice). Extensive experiments demonstrate that our approach can reliably detect the 3D positions of granular targets with small Root Mean Square Error (RMSE), high robustness to optical aberration and light scattering in mammalian brain tissues.
Issue Date: 2-Jun-2020
Date of Acceptance: 19-May-2020
URI: http://hdl.handle.net/10044/1/80567
DOI: 10.1109/TCI.2020.2997301
ISSN: 2333-9403
Publisher: IEEE
Start Page: 1017
End Page: 1032
Journal / Book Title: IEEE transactions on computational imaging
Volume: 6
Copyright Statement: © 2020 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/
Sponsor/Funder: Biotechnology and Biological Sciences Research Council (BBSRC)
Royal Academy Of Engineering
Engineering and Physical Sciences Research Council
Funder's Grant Number: BB/R009007/1
RF1415\14\26
EP/R512540/1
Publication Status: Published
Online Publication Date: 2020-05-29
Appears in Collections:Bioengineering
Electrical and Electronic Engineering
Faculty of Engineering



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