RT-DeCal: A hardware system for real-time decoding of in-vivo calcium imaging data

• Published in: bioRxiv
• Main Authors: Chen, Zhe, Blair, Garrett J, Guo, Changliang, Zhou, Jim, Izquierdo, Alicia, Golshani, Peyman, Cong, Jason, Aharoni, Daniel, Blair, Hugh T
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 02.03.2022
• Subjects: Calcium imaging; Calcium signalling; Hippocampus; Population
• DOI: 10.1101/2022.01.31.478424

Epifluorescence miniature microscopes ("miniscopes") are widely used for in vivo calcium imaging of neural population activity. Imaging data is usually collected while subjects are engaged in a task and stored for later offline analysis, but emerging techniques for online imaging offer potential for novel real-time experiments in which closed-loop interventions (such as neurostimulation or sensory feedback) are triggered at short latencies in response to neural population activity. Here we introduce RT-DeCal, a plug-and-play hardware device for online population decoding of in vivo calcium signals that can trigger closed-loop feedback at millisecond latencies, and is compatible with miniscopes that use the UCLA Data Acquisition (DAQ) interface. In performance tests, the position of rats (n=13) on a linear track was decoded in real time from hippocampal CA1 population activity by 24 linear classifiers. RT-DeCal required <2.5 ms after each end-of-frame to decode up to 1,024 calcium traces and trigger TTL control outputs. Decoding was most efficient using a 'contour-free' method of extracting traces from ROIs that were unaligned with neurons in the image, but 'contour-based' extraction from neuronal ROIs is also supported. RT-DeCal is an easy-to-use system for real-time decoding of calcium fluorescence that enables closed-loop feedback experiments in behaving animals. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://github.com/zhe-ch/ACTEV