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

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...

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Autores principales: Howe, Carmel L., Quicke, Peter, Song, Pingfan, Verinaz-Jadan, Herman, Dragotti, Pier Luigi, Foust, Amanda J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Society of Photo-Optical Instrumentation Engineers 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8922050/
https://www.ncbi.nlm.nih.gov/pubmed/35445141
http://dx.doi.org/10.1117/1.NPh.9.4.041404
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author Howe, Carmel L.
Quicke, Peter
Song, Pingfan
Verinaz-Jadan, Herman
Dragotti, Pier Luigi
Foust, Amanda J.
author_facet Howe, Carmel L.
Quicke, Peter
Song, Pingfan
Verinaz-Jadan, Herman
Dragotti, Pier Luigi
Foust, Amanda J.
author_sort Howe, Carmel L.
collection PubMed
description 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 confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson–Lucy three-dimensional 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 with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes. CONCLUSIONS: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly 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.
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spelling pubmed-89220502022-04-19 Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields Howe, Carmel L. Quicke, Peter Song, Pingfan Verinaz-Jadan, Herman Dragotti, Pier Luigi Foust, Amanda J. Neurophotonics Special Section on Computational Approaches for Neuroimaging 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 confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson–Lucy three-dimensional 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 with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes. CONCLUSIONS: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly 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. Society of Photo-Optical Instrumentation Engineers 2022-03-11 2022-10 /pmc/articles/PMC8922050/ /pubmed/35445141 http://dx.doi.org/10.1117/1.NPh.9.4.041404 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Special Section on Computational Approaches for Neuroimaging
Howe, Carmel L.
Quicke, Peter
Song, Pingfan
Verinaz-Jadan, Herman
Dragotti, Pier Luigi
Foust, Amanda J.
Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
title Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
title_full Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
title_fullStr Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
title_full_unstemmed Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
title_short Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
title_sort comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
topic Special Section on Computational Approaches for Neuroimaging
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8922050/
https://www.ncbi.nlm.nih.gov/pubmed/35445141
http://dx.doi.org/10.1117/1.NPh.9.4.041404
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