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.
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We thank K. P. Nguyen for the animal illustrations. This work was supported by the Agency for Science, Technology and Research (A*STAR) Singapore (T.H.K.), Howard Hughes Medical Institute (W.E.B., T.K., Z.W. and M.B.A.), Simons Foundation Simons Collaboration on the Global Brain Award 542943 (M.B.A.) and 543065 (B.M.Y.), the Shurl and Kay Curci Foundation (S.M.C. and S.J.K.), NIH R01 HD071686 (S.M.C. and B.M.Y.), NIH R01 EY024678 (S.J.K.), NSF NCS BCS1533672 (S.M.C. and B.M.Y.), NSF CAREER award IOS1553252 (S.M.C.), NSF NCS DRL2124066 (B.M.Y. and S.M.C.), NSF NCS BCS1734916 (B.M.Y.), NIH CRCNS R01 NS105318 (B.M.Y.), NIH CRCNS R01 MH118929 (B.M.Y.) and NIH R01 EB026953 (B.M.Y.).
The authors declare no competing interests.
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Koh, T.H., Bishop, W.E., Kawashima, T. et al. Dimensionality reduction of calcium-imaged neuronal population activity. Nat Comput Sci 3, 71–85 (2023). https://doi.org/10.1038/s43588-022-00390-2