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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Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR

Nature Methods, Год журнала: 2018, Номер 15(11), С. 936 - 939

Опубликована: Окт. 19, 2018

Язык: Английский

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Pushing the frontiers: tools for monitoring neurotransmitters and neuromodulators

Nature reviews. Neuroscience, Год журнала: 2022, Номер 23(5), С. 257 - 274

Опубликована: Март 31, 2022

Язык: Английский

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Kilohertz frame-rate two-photon tomography

Nature Methods, Год журнала: 2019, Номер 16(8), С. 778 - 786

Опубликована: Июль 29, 2019

Язык: Английский

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Specialized astrocytes mediate glutamatergic gliotransmission in the CNS

Nature, Год журнала: 2023, Номер 622(7981), С. 120 - 129

Опубликована: Сен. 6, 2023

Abstract Multimodal astrocyte–neuron communications govern brain circuitry assembly and function 1 . For example, through rapid glutamate release, astrocytes can control excitability, plasticity synchronous activity 2,3 of synaptic networks, while also contributing to their dysregulation in neuropsychiatric conditions 4–7 communicate fast focal they should possess an apparatus for Ca 2+ -dependent exocytosis similar neurons 8–10 However, the existence this mechanism has been questioned 11–13 owing inconsistent data 14–17 a lack direct supporting evidence. Here we revisited astrocyte hypothesis by considering emerging molecular heterogeneity 18–21 using molecular, bioinformatic imaging approaches, together with cell-specific genetic tools that interfere vivo. By analysing existing single-cell RNA-sequencing databases our patch-seq data, identified nine molecularly distinct clusters hippocampal astrocytes, among which found notable subpopulation selectively expressed synaptic-like glutamate-release machinery localized discrete sites. Using GluSnFR-based 22 situ vivo, corresponding subgroup responds reliably astrocyte-selective stimulations subsecond release events at spatially precise hotspots, were suppressed astrocyte-targeted deletion vesicular transporter (VGLUT1). Furthermore, or its isoform VGLUT2 revealed specific contributions glutamatergic cortico-hippocampal nigrostriatal circuits during normal behaviour pathological processes. uncovering atypical specialized adult brain, provide insights into complex roles central nervous system (CNS) physiology diseases, identify potential therapeutic target.

Язык: Английский

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Mesoscale Mapping of Mouse Cortex Reveals Frequency-Dependent Cycling between Distinct Macroscale Functional Modules

Journal of Neuroscience, Год журнала: 2017, Номер 37(31), С. 7513 - 7533

Опубликована: Июль 3, 2017

Connectivity mapping based on resting-state activity in mice has revealed functional motifs of correlated activity. However, the rules by which organize into larger modules that lead to hemisphere wide spatial-temporal sequences is not clear. We explore cortical parcellation head-fixed, quiet awake GCaMP6 from both sexes using mesoscopic calcium imaging. Spectral decomposition spontaneous presence two dominant frequency modes (<1 and ∼3 Hz), each them associated with a unique spatial signature macro-parcellation predicted classical cytoarchitectonic definitions areas. Based assessment 0.1–1 Hz activity, we define macro-organizing principles: first being rotating polymodal-association pinwheel structure around flows sequentially visual barrel then hindlimb somatosensory; second principle symmetry planes exist many levels within single domain such as intrahemispheric reflections sensory motor cortices. In contrast, higher >1 yielded clusters coactivated areas an enlarged default mode network-like posterior region. suggest apparent constrained for intra-areal flow could be exploited future efforts normalize diseases nervous system. SIGNIFICANCE STATEMENT Increasingly, connectivity used reveal organization brain. because brain operates across multiple space time domains more detailed understanding this necessary. in vivo wide-field imaging indicator characterize at different spatiotemporal scales. Correlation analysis defines three superclusters span traditionally defined territories were dependent. This work helps how interact space. provide framework necessary studies reorganization circuits disease models.

Язык: Английский

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Ultrafast glutamate sensors resolve high-frequency release at Schaffer collateral synapses

Proceedings of the National Academy of Sciences, Год журнала: 2018, Номер 115(21), С. 5594 - 5599

Опубликована: Май 7, 2018

Significance Excitatory synapses convert presynaptic action potentials into chemical signals that are sensed by postsynaptic glutamate receptors. To eavesdrop on synaptic transmission, genetically encoded fluorescent sensors for have been developed. However, even the best available lag behind very fast dynamics in cleft. Here, we report development of an ultrafast sensor, iGlu u , which allowed us to image clearance and depression during 100-Hz spike trains. We found only boutons showing paired-pulse facilitation were able rapidly recover from depression. Thus, act as frequency-specific filters transmit select features train specific cells.

Язык: Английский

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Learning in the Rodent Motor Cortex

Annual Review of Neuroscience, Год журнала: 2017, Номер 40(1), С. 77 - 97

Опубликована: Апрель 4, 2017

The motor cortex is far from a stable conduit for commands and instead undergoes significant changes during learning. An understanding of plasticity has been advanced greatly using rodents as experimental animals. Two major focuses this research have on the connectivity activity cortex. exhibits structural in response to learning, substantial evidence implicated local formation maintenance new synapses crucial substrates This synaptic reorganization translates into spiking activity, which appear result modification refinement relationship between cortical movement. review presents progress that made establish an adaptive structure supports

Язык: Английский

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Mapping cortical mesoscopic networks of single spiking cortical or sub-cortical neurons

eLife, Год журнала: 2017, Номер 6

Опубликована: Фев. 4, 2017

Understanding the basis of brain function requires knowledge cortical operations over wide-spatial scales, but also within context single neurons. In vivo, wide-field GCaMP imaging and sub-cortical/cortical cellular electrophysiology were used in mice to investigate relationships between spontaneous neuron spiking mesoscopic activity. We make use a rich set activity motifs that are present anesthetized awake animals. A mesoscale spike-triggered averaging procedure allowed identification preferentially linked individual neurons by employing genetically targeted indicators neuronal Thalamic predicted reported specific cycles wide-scale inhibition/excitation. contrast, maps derived from yielded spatio-temporal expected for regional consensus function. This approach can define network any point source maps.

Язык: Английский

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