Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Feb 22, 2018
- Source ID
- 10.7554/elife.28728
Entities
People
- Andrea Giovannucci
- Bernardo L. Sabatini
- Eftychios A Pnevmatikakis
- Garret D. Stuber
- Jessica C. Jimenez
- Johannes Friedrich
- Jose Rodriguez-romaguera
- Liam Paninski
- Mazen A. Kheirbek
- Pengcheng Zhou
- René Hen
- Robert E. Kass
- Shanna L Resendez
- Shay Q Neufeld
Organizations
- Army Research Office
- Canadian Institutes of Health Research
- Carnegie Mellon University
- Columbia University
- Defense Advanced Research Projects Agency
- Eunice Kennedy Shriver National Institute of Child Health and Human Development
- Flatiron Institute
- Harvard Medical School
- Hope for Depression Research Foundation
- Howard Hughes Medical Institute
- Intelligence Advanced Research Projects Activity
- International Mental Health Research Organization
- National Institute of Biomedical Imaging and Bioengineering
- National Institute of Mental Health
- National Institute of Neurological Disorders and Stroke
- National Institute on Aging
- National Institute on Drug Abuse
- New York State Psychiatric Institute
- Simons Foundation
- University of California
- University of California, San Francisco
- University of North Carolina at Chapel Hill