Dimensionality reduction of calcium-imaged neuronal population activity

Calcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality-reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear whether the dimensionality-reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality-reduction methods. We have also developed a method to perform deconvolution and dimensionality reduction simultaneously (calcium imaging linear dynamical system, CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from simulated calcium imaging data. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium-imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.