Effective and Efficient Neural Networks for Spike Inference from In Vivo Calcium Imaging

• Published in: bioRxiv
• Main Authors: Zhou, Zhanhong, Yip, Hei Matthew, Tsimring, Katya, Sur, Mriganka, Jacque Pak Kan Ip, Chung, Tin
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 15.10.2022
• Subjects: Calcium imaging; Calcium signalling; Electrophysiology; Firing pattern; Firing rate; Information processing; Nervous system; Neural networks; Neuroimaging; Orientation behavior; Predictions; Visual cortex
• DOI: 10.1101/2021.08.30.458217

Calcium imaging technique provides the advantages in monitoring large population of neuronal activities simultaneously. However, it lacks the signal quality provided by neural spike recording in traditional electrophysiology. To address this issue, we developed a supervised data-driven approach to extract spike information from calcium signals. We propose the ENS2 (effective and efficient neural networks for spike inference from calcium signals) system for spike-rate and spike-event predictions using raw calcium inputs based on U-Net deep neural network. When testing on a large, ground truth public database, it consistently outperformed state-of-the-arts algorithms in both spike-rate and spike-event predictions with reduced computational load. We further demonstrated that ENS2 would improve analyses of orientation selectivity in primary visual cortex neurons. We concluded that it would be a versatile inference system that benefits diverse neuroscience studies. Competing Interest Statement The authors have declared no competing interest. Footnotes * Version 3