Dimensionality reduction of calcium-imaged neuronal population activity

Tze Hui Koh, William E Bishop, Takashi Kawashima, Brian B Jeon, Ranjani Srinivasan, Sandra J Kuhlman, Misha B. Ahrens, Steven M. Chase, Byron M. Yu

Research output: Contribution to journalArticlepeer-review


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 if 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 also developed a novel method to perform deconvolution and dimensionality reduction simultaneously (termed CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from calcium imaging that would have been recovered from spiking activity. 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.
Original languageEnglish
Number of pages15
JournalNature Computational Science
StatePublished - 29 Dec 2022


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