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Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data
Open accessAbstract
SUMMARY We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in vitro and in vivo multineuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data.
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Ultrasensitive fluorescent proteins for imaging neuronal activity
Chen, T.-W., Wardill, T. J., Sun, Y., Pulver, S. R., Renninger, S. L., Baohan, A., Schreiter, E. R., Kerr, R. A., Orger, M. B., Jayaraman, V., et al. (2013) · Nature · doi:10.1038/nature12354 · Cited by 6,474
Fast nonnegative deconvolution for spike train inference from population calcium imaging
Vogelstein, J. T., Packer, A. M., Machado, T. A., Sippy, T., Babadi, B., Yuste, R., & Paninski, L. (2010) · Journal of Neurophysiology · doi:10.1152/jn.01073.2009 · Cited by 449
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Self-citationDynamic Reorganization of Neuronal Activity Patterns in Parietal Cortex
Driscoll, L. N., Pettit, N. L., Minderer, M., Chettih, S. N., & Harvey, C. D. (2017) · Cell · doi:10.1016/j.cell.2017.07.021 · Cited by 445
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Metadata
- Authors
- Pnevmatikakis, E. A., Soudry, D., Gao, Y., Machado, T. A., Merel, J., Pfau, D., Reardon, T., Mu, Y., Lacefield, C., Yang, W., Ahrens, M., Bruno, R., Jessell, T. M., Peterka, D. S., Yuste, R., & Paninski, L.
- Venue
- Neuron
- Publisher
- Elsevier BV
- Published
- 2016-01
- Volume
- 89
- Issue
- 2
- Pages
- 285-299
- ISSN
- 0896-6273 (ISSN-L)
- OpenAlex
- W2231009150
- Cited by
- 1,029
- References
- 2
- FWCI
- 57.75
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Pnevmatikakis, E. A., Soudry, D., Gao, Y., Machado, T. A., Merel, J., Pfau, D., Reardon, T., Mu, Y., Lacefield, C., Yang, W., Ahrens, M., Bruno, R., Jessell, T. M., Peterka, D. S., Yuste, R., & Paninski, L. (2016). Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data. Neuron. https://doi.org/10.1016/j.neuron.2015.11.037
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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
