Skip to main content
eScholarship
Open Access Publications from the University of California

UCSF

UC San Francisco Previously Published Works bannerUCSF

Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data.

  • Author(s): Zhou, Pengcheng
  • Resendez, Shanna L
  • Rodriguez-Romaguera, Jose
  • Jimenez, Jessica C
  • Neufeld, Shay Q
  • Giovannucci, Andrea
  • Friedrich, Johannes
  • Pnevmatikakis, Eftychios A
  • Stuber, Garret D
  • Hen, Rene
  • Kheirbek, Mazen A
  • Sabatini, Bernardo L
  • Kass, Robert E
  • Paninski, Liam
  • et al.
Abstract

In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We compared the proposed method against previous independent components analysis and constrained nonnegative matrix factorization approaches. On both simulated and experimental data recorded from mice, our method substantially improved the quality of extracted cellular signals and detected more well-isolated neural signals, especially in noisy data regimes. These advances can in turn significantly enhance the statistical power of downstream analyses, and ultimately improve scientific conclusions derived from microendoscopic data.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View