The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Suite2p: beyond 10,000 neurons with standard two-photon microscopy
Open accessAbstract
Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.
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Cites
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Matching pursuits with time-frequency dictionaries
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Ultrasensitive fluorescent proteins for imaging neuronal activity
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Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data
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NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data
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Extension of phase correlation to subpixel registration
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A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging
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Cited by
Spontaneous behaviors drive multidimensional, brainwide activity
Stringer, C., Pachitariu, M., Steinmetz, N., Reddy, C. B., Carandini, M., & Harris, K. D. (2019) · Science · doi:10.1126/science.aav7893 · Cited by 1,510
Self-citationNeuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings.
Steinmetz, N. A., Aydin, C., Lebedeva, A., Okun, M., Pachitariu, M., Bauza, M., Beau, M., Bhagat, J., Böhm, C., Broux, M., et al. (2021) · Science · doi:10.1126/science.abf4588 · Cited by 1,173
“To correct for nonrigid drift, we again turn to a common practice in image analysis: splitting the data into multiple segments and assuming approximately rigid drift for each small segment (Pachitariu et al., 2017).”
MethodSelf-citationSingle-trial neural dynamics are dominated by richly varied movements
Musall, S., Kaufman, M. T., Juavinett, A. L., Gluf, S., & Churchland, A. K. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0502-4 · Cited by 1,075
Negative feedback control of neuronal activity by microglia
Badimon, A., Strasburger, H. J., Ayata, P., Chen, X., Nair, A., Ikegami, A., Hwang, P., Chan, A. T., Graves, S. M., Uweru, J. O., et al. (2020) · Nature · doi:10.1038/s41586-020-2777-8 · Cited by 979
Fast and sensitive GCaMP calcium indicators for imaging neural populations
Zhang, Y., Rózsa, M., Liang, Y., Bushey, D., Wei, Z., Zheng, J., Reep, D., Broussard, G. J., Tsang, A., Tsegaye, G., et al. (2023) · Nature · doi:10.1038/s41586-023-05828-9 · Cited by 870
Metadata
- Authors
- Pachitariu, M., Stringer, C., Dipoppa, M., Schröder, S., Rossi, L. F., Dalgleish, H., Carandini, M., & Harris, K. D.
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2016-06-30
- OpenAlex
- W2469581795
- Cited by
- 1,247
- References
- 32
- Type
- posted content
- Language
- en
- Open access
- green
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