BibTex format

author = {Howe, C and Song, P and Verinaz, Jadan HI and Dragotti, PL and Quicke, P and Foust, A},
doi = {10.1117/1.NPh.9.4.041404},
journal = {Neurophotonics},
pages = {1--17},
title = {Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields},
url = {},
volume = {9},
year = {2022}

RIS format (EndNote, RefMan)

AB - 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.
AU - Howe,C
AU - Song,P
AU - Verinaz,Jadan HI
AU - Dragotti,PL
AU - Quicke,P
AU - Foust,A
DO - 10.1117/1.NPh.9.4.041404
EP - 17
PY - 2022///
SN - 2329-4248
SP - 1
TI - Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
T2 - Neurophotonics
UR -
UR -
UR -
VL - 9
ER -