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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2016, Номер unknown

Опубликована: Июнь 30, 2016

Abstract Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations neurons. While the and microscopes have matured over several generations development, computational methods to process resulting movies remain inefficient can give results that are hard interpret. Here we introduce Suite2p: a fast, accurate complete pipeline registers raw movies, detects active cells, extracts their calcium traces infers spike times. Suite2p runs on standard workstations, operates faster than real time, recovers ~2 times more cells previous state-of-the-art method. Its low load allows routine detection ~10,000 simultaneously with two-photon resonant-scanning microscopes. Recordings at this scale promise reveal fine structure activity in large neurons or subcellular structures such as synaptic boutons.

Язык: Английский

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CaImAn an open source tool for scalable calcium imaging data analysis

eLife, Год журнала: 2019, Номер 8

Опубликована: Янв. 14, 2019

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging analysis. CaImAn provides automatic methods address problems common pre-processing, including motion correction, neural activity identification, registration across different sessions collection. It does this while requiring minimal user intervention, good scalability on computers ranging from laptops high-performance computing clusters. is suitable two-photon one-photon imaging, also enables real-time streaming data. To benchmark performance we collected combined a corpus manual annotations multiple labelers nine mouse datasets. demonstrate achieves near-human detecting locations active neurons.

Язык: Английский

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Genetically encoded indicators of neuronal activity

Nature Neuroscience, Год журнала: 2016, Номер 19(9), С. 1142 - 1153

Опубликована: Авг. 26, 2016

Язык: Английский

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Fast online deconvolution of calcium imaging data

PLoS Computational Biology, Год журнала: 2017, Номер 13(3), С. e1005423 - e1005423

Опубликована: Март 14, 2017

Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting each neuron from raw fluorescence imaging data is nontrivial problem. We present fast online active set method to solve this sparse non-negative deconvolution Importantly, algorithm progresses through time series sequentially beginning end, thus enabling real-time estimation neural during session. Our generalization pool adjacent violators (PAVA) isotonic regression and inherits its linear-time computational complexity. gain remarkable increases in processing speed: more than one order magnitude compared currently employed state art convex solvers relying on interior point methods. Unlike these approaches, our can exploit warm starts; therefore optimizing model hyperparameters only requires handful passes data. A minor modification further improve quality inference by imposing constraint minimum spike size. The enables simultaneous $O(10^5)$ traces whole-brain larval zebrafish laptop.

Язык: Английский

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Genetic Dissection of Neural Circuits: A Decade of Progress

Neuron, Год журнала: 2018, Номер 98(2), С. 256 - 281

Опубликована: Апрель 1, 2018

Tremendous progress has been made since Neuron published our Primer on genetic dissection of neural circuits 10 years ago. Since then, cell-type-specific anatomical, neurophysiological, and perturbation studies have carried out in a multitude invertebrate vertebrate organisms, linking neurons to behavioral functions. New methods allow systematic classification cell types provide access diverse neuronal for connectivity coding during behavior. Here we evaluate key advances over the past decade discuss future directions.

Язык: Английский

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In vivo imaging of neural activity

Nature Methods, Год журнала: 2017, Номер 14(4), С. 349 - 359

Опубликована: Март 31, 2017

Язык: Английский

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Tracking the Same Neurons across Multiple Days in Ca2+ Imaging Data

Cell Reports, Год журнала: 2017, Номер 21(4), С. 1102 - 1115

Опубликована: Окт. 1, 2017

Ca2+ imaging techniques permit time-lapse recordings of neuronal activity from large populations over weeks. However, without identifying the same neurons across sessions (cell registration), longitudinal analysis neural code is restricted to population-level statistics. Accurate cell registration becomes challenging with increased numbers cells, sessions, and inter-session intervals. Current practices, whether manual or automatic, do not quantitatively evaluate accuracy, possibly leading data misinterpretation. We developed a probabilistic method that automatically registers cells multiple estimates confidence for each registered cell. Using large-scale recorded weeks hippocampus cortex freely behaving mice, we show our performs more accurate than previously used routines, yielding estimated error rates <5%, scalable many sessions. Thus, allows reliable long time periods.

Язык: Английский

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Transformation of Cortex-wide Emergent Properties during Motor Learning

Neuron, Год журнала: 2017, Номер 94(4), С. 880 - 890.e8

Опубликована: Май 1, 2017

Язык: Английский

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Improving data quality in neuronal population recordings

Nature Neuroscience, Год журнала: 2016, Номер 19(9), С. 1165 - 1174

Опубликована: Авг. 26, 2016

Язык: Английский

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Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Июль 19, 2016

Abstract Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals vivo , where large noises often contaminate the signals. We propose a method, MLspike, which returns most likely spike train underlying measured calcium fluorescence. It relies on physiological model including baseline fluctuations and distinct nonlinearities for synthetic genetically encoded indicators. Model parameters can be either provided by user or estimated data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it also return probabilities samples. Benchmarked extensive simulations real seven different preparations, outperformed state-of-the-art algorithms. Combined with finding obtained systematic investigation (noise level, rate so on) that photonic noise not necessarily main limiting factor, our method allows extraction recordings, as demonstrated acousto-optical three-dimensional over 1,000 neurons .

Язык: Английский

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