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Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields

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Title: Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
Authors: Howe, C
Song, P
Verinaz Jadan, HI
Dragotti, PL
Quicke, P
Foust, A
Item Type: Journal Article
Abstract: Significance: Light-field microscopy (LFM) enables fast, light-efficient, volumetric imaging of neuronal activity with calcium indicators. Calcium transients differ in temporal signal-to-noise ratio (tSNR) and spatial confinement when extracted from volumes reconstructed by different algorithms. Aim: We evaluated the capabilities and limitations of two light-field reconstruction algorithms for calcium fluorescence imaging. Approach: We acquired light-field image series from neurons either bulk-labeled or filled intracellularly with the red-emitting calcium dye CaSiR-1 in acute mouse brain slices. We compared the tSNR and spatial onfinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson-Lucy 3D deconvolution with and without total variation regularization. Results: Both synthetic refocusing and Richardson-Lucy deconvolution resolved calcium signals from single cells and neuronal dendrites in three dimensions. Increasing deconvolution iteration number improved spatial confinement but reduced tSNR compared to synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared to interleaved, widefield image series acquired in matched planes. Conclusions: LFM enables high-volume rate, volumetric imaging of calcium transients in single cells (bulk-labeled), somata and dendrites (intracellular loaded). The trade-offs identified for tSNR, spatial confinement, and computational cost indicate which of synthetic refocusing or deconvolution can better realize the scientific requirements of future LFM calcium imaging applications.
Issue Date: 11-Mar-2022
Date of Acceptance: 7-Feb-2022
URI: http://hdl.handle.net/10044/1/95264
DOI: 10.1117/1.NPh.9.4.041404
ISSN: 2329-4248
Publisher: Society of Photo-optical Instrumentation Engineers
Start Page: 1
End Page: 17
Journal / Book Title: Neurophotonics
Volume: 9
Issue: 4
Copyright Statement: © The Authors. Published by SPIE under a Creative Commons Attribution 4.0 International License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI. [DOI: 10.1117/1.NPh.9.4.041404]
Sponsor/Funder: Royal Academy Of Engineering
Wellcome Trust
Biotechnology and Biological Sciences Research Council (BBSRC)
Biotechnology and Biological Sciences Research Council (BBSRC)
National Institutes of Health
Funder's Grant Number: RF1415\14\26
201964/Z/16/Z
BB/R009007/1
EP/V520354/1
UPMC: C15/0244
Keywords: calcium imaging
deconvolution
fluorescence imaging
light-field microscopy
0903 Biomedical Engineering
1004 Medical Biotechnology
1109 Neurosciences
Publication Status: Published
Online Publication Date: 2022-03-11
Appears in Collections:Bioengineering
Electrical and Electronic Engineering
Faculty of Engineering



This item is licensed under a Creative Commons License Creative Commons