Suite2p: beyond 10,000 neurons with standard two-photon microscopy

By Marius Pachitariu, C. Stringer, Mario Dipoppa, Sylvia Schröder, L. F. Rossi, Henry W. P. Dalgleish, Matteo Carandini, Kenneth D. Harris. bioRxiv, 2016

1,087 citations recorded by the source corpus.

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.

Subfields: Biophysics, Media Technology

View Paper: https://www.semanticscholar.org/paper/3b435983c5bb6c77028fb5870ab7ad3bda273dff

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Citations in the corpus

Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data (2018, neutral): “(See [Pachitariu et al., 2016] for an alter- native approach.)”
Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis (2017, background): “Recent experimental advances enable us to monitor all aspects of this complexity by recording large numbers of neurons at high temporal precision (Marblestone et al., 2013; Kim et al., 2016; Lin and Schnitzer, 2016; Pachitariu et al., 2016; Jun et al., 2017) over long durations (L€ utcke et al.”
Spontaneous Behaviors Drive Multidimensional, Brain-wide Activity (2019, methodology): “The preprocessing of all raw calcium movie data was done using a toolbox we developed called Suite2p, using the default settings (29).”
Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings (2020, methodology): “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).”
NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data (2017, methodology): “dealing with non-rigid motion in the context of calcium imaging data, available 22 approaches include the work of Greenberg & Kerr [6] which is based on the 23 Lucas-Kanade method [9], Hidden Markov Models (HMM) [2, 8] approaches, 24 and block rigid registration [11].”
Scalable Bayesian GPFA with automatic relevance determination and discrete noise models (2021, positive): “The robustness to overfitting of bGPFA both with and without ARD suggests that it could also be a valuable tool in settings with large simultaneous recordings of thousands of neurons, which are becoming increasingly relevant with recent advances in neural recording technologies (Steinmetz et al., 20”
Tracking the Same Neurons across Multiple Days in Ca2+ Imaging Data (2017, methodology): “The registration procedure is fully automated and does not require manual inspection of each cell, making it scalable for very large FOVs (Kim et al., 2016; Pachitariu et al., 2016; Sofroniew et al., 2016).”
Fast online deconvolution of calcium imaging data (2016, methodology): “However, recently several investigators [46, 47, 48] have advocated sparser methods, e.g. by using an (cid:96) q -norm with q 1 instead of q = 1 [46] or by enforcing refractoriness [47] (see also [13] for some further discussion of sparsening beyond (cid:96) 1 penalization).”