CaImAn an open source tool for scalable calcium imaging data analysis

eLife, Journal Year: 2019, Volume and Issue: 8

Published: Jan. 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.

Language: Английский

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Genetic Dissection of Neural Circuits: A Decade of Progress

Neuron, Journal Year: 2018, Volume and Issue: 98(2), P. 256 - 281

Published: April 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.

Language: Английский

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Apolipoprotein E Binding Drives Structural and Compositional Rearrangement of mRNA-Containing Lipid Nanoparticles

ACS Nano, Journal Year: 2021, Volume and Issue: 15(4), P. 6709 - 6722

Published: March 23, 2021

Emerging therapeutic treatments based on the production of proteins by delivering mRNA have become increasingly important in recent times. While lipid nanoparticles (LNPs) are approved vehicles for small interfering RNA delivery, there still challenges to use this formulation delivery. LNPs typically a mixture cationic lipid, distearoylphosphatidylcholine (DSPC), cholesterol, and PEG-lipid. The structural characterization mRNA-containing (mRNA-LNPs) is crucial full understanding way which they function, but information alone not enough predict their fate upon entering bloodstream. biodistribution cellular uptake affected surface composition as well extracellular present at site LNP administration,

Language: Английский

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Robustness of Spike Deconvolution for Neuronal Calcium Imaging

Journal of Neuroscience, Journal Year: 2018, Volume and Issue: 38(37), P. 7976 - 7985

Published: Aug. 6, 2018

Calcium imaging is a powerful method to record the activity of neural populations in many species, but inferring spike times from calcium signals challenging problem. We compared multiple approaches using datasets with ground truth electrophysiology and found that simple non-negative deconvolution (NND) outperformed all other algorithms on out-of-sample test data. introduce novel benchmark applicable recordings without electrophysiological truth, based correlation responses two stimulus repeats, used this show unconstrained NND also when run “zoomed out” ∼10,000 cell visual cortex mice either sex. Finally, we NND-based methods match performance supervised convolutional networks while avoiding some biases such methods, at much faster running times. therefore recommend spikes be inferred traces because its simplicity, efficiency, accuracy. SIGNIFICANCE STATEMENT The experimental currently allows for largest numbers cells simultaneously two-photon imaging. However, use requires neuronal firing correctly large resulting datasets. Previous studies have claimed complex learning outperform task. Unfortunately, these suffered several problems biases. When repeated analysis, same data correcting problems, simpler inference perform better. Even more importantly, can artifactual structure into trains, which turn lead erroneous scientific conclusions. Of evaluated, an extremely performed best circumstances tested, was run, insensitive parameter choices, making incorrect conclusions less likely.

Language: Английский

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Learnable latent embeddings for joint behavioural and neural analysis

Nature, Journal Year: 2023, Volume and Issue: 617(7960), P. 360 - 368

Published: May 3, 2023

Abstract Mapping behavioural actions to neural activity is a fundamental goal of neuroscience. As our ability record large and data increases, there growing interest in modelling dynamics during adaptive behaviours probe representations 1–3 . In particular, although latent embeddings can reveal underlying correlates behaviour, we lack nonlinear techniques that explicitly flexibly leverage joint behaviour uncover 3–5 Here, fill this gap with new encoding method, CEBRA, jointly uses (supervised) hypothesis- or (self-supervised) discovery-driven manner produce both consistent high-performance spaces. We show consistency be used as metric for uncovering meaningful differences, the inferred latents decoding. validate its accuracy demonstrate tool’s utility calcium electrophysiology datasets, across sensory motor tasks simple complex species. It allows single- multi-session datasets hypothesis testing label free. Lastly, CEBRA mapping space, kinematic features, production spaces two-photon Neuropixels data, provide rapid, high-accuracy decoding natural videos from visual cortex.

Language: Английский

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Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

eLife, Journal Year: 2021, Volume and Issue: 10

Published: March 8, 2021

Fluorescent calcium indicators are often used to investigate neural dynamics, but the relationship between fluorescence and action potentials (APs) remains unclear. Most APs can be detected when soma almost fills microscope's field of view, image populations neurons, necessitating a large generating fewer photons per neuron, compromising AP detection. Here, we characterized AP-fluorescence transfer function in vivo for 48 layer 2/3 pyramidal neurons primary visual cortex, with simultaneous imaging cell-attached recordings from transgenic mice expressing GCaMP6s or GCaMP6f. While most were under optimal conditions, conditions typical population studies, only minority 1 2 events (often <10% ~20-30%, respectively), emphasizing limits detection more realistic conditions.Neurons, cells that make up nervous system, transmit information using electrical signals known as spikes. Studying spiking patterns brain is essential understand perception, memory, thought, behaviour. One way do by recording activity microelectrodes. Another study neuronal molecules change how they interact light binds them, since changes concentration indicative spiking. That observed specialized microscopes know two-photon microscopes. Using indicators, it possible simultaneously record hundreds even thousands neurons. However, spikes not translate one-to-one. In order interpret data, important associated individual The directly measure this same neuron. extremely challenging experimentally, so type data rare. To shed some on this, Huang, Ledochowitsch et al. had been genetically modified produce indicator cortex obtained both measurements these These experiments revealed that, while majority time periods containing multi-spike could identified microscopy, average, less than 10% isolated single detectable. This an caveat researchers need take into consideration interpreting results. findings intended serve guide studies look at mammalian level. addition, provided will useful reference development sensors, benchmark improve computational approaches detecting predicting

Language: Английский

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A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(9), P. e1008198 - e1008198

Published: Sept. 15, 2020

Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural and calcium-related fluorescence involves nonlinearities low-pass filtering, but the effects of transformation on analyses populations are not well understood. We compared spikes matched behaving mice. report multiple discrepancies performed two types data, including changes single-neuron selectivity population decoding. These were only partially resolved by spike inference algorithms applied fluorescence. To model relation spiking we simultaneously recorded from individual neurons. Using these recordings developed a transforming trains synthetic-imaging data. recapitulated differences analyses. Our analysis highlights challenges relating electrophysiology suggests forward modeling as an effective way understand

Language: Английский

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Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising

Nature Methods, Journal Year: 2021, Volume and Issue: 18(11), P. 1395 - 1400

Published: Aug. 16, 2021

Language: Английский

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A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging

Nature Neuroscience, Journal Year: 2021, Volume and Issue: 24(9), P. 1324 - 1337

Published: Aug. 2, 2021

Language: Английский

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Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy

Cell, Journal Year: 2022, Volume and Issue: 185(18), P. 3408 - 3425.e29

Published: Aug. 18, 2022

Genetically encoded voltage indicators are emerging tools for monitoring dynamics with cell-type specificity. However, current enable a narrow range of applications due to poor performance under two-photon microscopy, method choice deep-tissue recording. To improve indicators, we developed multiparameter high-throughput platform optimize microscopy. Using this system, identified JEDI-2P, an indicator that is faster, brighter, and more sensitive photostable than its predecessors. We demonstrate JEDI-2P can report light-evoked responses in axonal termini Drosophila interneurons the dendrites somata amacrine cells isolated mouse retina. also optically record individual cortical neurons awake behaving mice 30 min using both resonant-scanning ULoVE random-access Finally, recording robustly detect spikes at depths exceeding 400 μm correlations pairs neurons.

Language: Английский

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