1. High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo
- Author
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Karel Svoboda, Liam Paninski, Linlin Z. Fan, Márton Rózsa, Adam E. Cohen, Ian Kinsella, Yoav Adam, Ding Zhou, Michael E. Xie, Urs Lucas Böhm, and Amrita Singh
- Subjects
0301 basic medicine ,Fluorescence-lifetime imaging microscopy ,Pipeline (computing) ,Action Potentials ,Mice, Transgenic ,Hippocampus ,General Biochemistry, Genetics and Molecular Biology ,Article ,Matrix decomposition ,03 medical and health sciences ,0302 clinical medicine ,High fidelity ,Imaging, Three-Dimensional ,Waveform ,Animals ,Computer Simulation ,lcsh:QH301-705.5 ,Zebrafish ,Physics ,Photons ,Subthreshold conduction ,Noise (signal processing) ,Pyramidal Cells ,Reproducibility of Results ,signal extraction ,030104 developmental biology ,lcsh:Biology (General) ,Biological system ,030217 neurology & neurosurgery ,Algorithms ,Voltage ,voltage imaging ,Signal Transduction - Abstract
Summary The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.
- Published
- 2020