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

Abstract

Light field microscopy (LFM) enables fast, light efficient, volumetric imaging of neuronal activity with functional fluorescence indicators. Here we apply LFM to single-cell and bulk-labeled imaging of the red calcium dye, CaSiR-1 in acute mouse brain slices. We compare two common light field volume reconstruction algorithms: synthetic refocusing and Richardson-Lucy 3D deconvolution. We compare temporal signal-to-noise ratio (SNR) and spatial signal confinement between the two LFM algorithms and conventional widefield image series. Both algorithms can resolve calcium signals from neuronal processes in three dimensions. Increasing deconvolution iteration number improves spatial signal confinement but reduces SNR compared to synthetic refocusing.