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bioRxiv · 10.1101/2022.01.31.478424

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

Chen, Z.·Blair, G. J.·Guo, C.·Izquierdo, A.·Golshani, P.·Cong, J.·Aharoni, D.·Blair, H. T.
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Abstract

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 DeCalciOn, 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. DeCalciOn 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. DeCalciOn is an easy-to-use system for real-time decoding of calcium fluorescence that enables closed-loop feedback experiments in behaving animals.

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Chen, Z., Blair, G. J., Guo, C., Izquierdo, A., Golshani, P., Cong, J., Aharoni, D., Blair, H. T.. 2022-02-02. A hardware system for real-time decoding of in-vivo calcium imaging data. https://doi.org/10.1101/2022.01.31.478424

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