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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Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

eLife, Год журнала: 2018, Номер 7

Опубликована: Фев. 22, 2018

In vivo calcium imaging through microendoscopic lenses enables of previously inaccessible neuronal populations deep within the brains freely moving animals. However, it is computationally challenging to extract single-neuronal activity from data, because very large background fluctuations and high spatial overlaps intrinsic this recording modality. Here, we describe a new constrained matrix factorization approach accurately separate then demix denoise signals interest. We compared proposed method against previous independent components analysis nonnegative approaches. On both simulated experimental data recorded mice, our substantially improved quality extracted cellular detected more well-isolated neural signals, especially in noisy regimes. These advances can turn significantly enhance statistical power downstream analyses, ultimately improve scientific conclusions derived data.

Язык: Английский

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Dopamine neuron activity before action initiation gates and invigorates future movements

Nature, Год журнала: 2018, Номер 554(7691), С. 244 - 248

Опубликована: Янв. 31, 2018

Язык: Английский

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Anxiety Cells in a Hippocampal-Hypothalamic Circuit

Neuron, Год журнала: 2018, Номер 97(3), С. 670 - 683.e6

Опубликована: Янв. 31, 2018

Язык: Английский

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The Striatum Organizes 3D Behavior via Moment-to-Moment Action Selection

Cell, Год журнала: 2018, Номер 174(1), С. 44 - 58.e17

Опубликована: Май 17, 2018

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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Maturation and circuit integration of transplanted human cortical organoids

Nature, Год журнала: 2022, Номер 610(7931), С. 319 - 326

Опубликована: Окт. 12, 2022

Abstract Self-organizing neural organoids represent a promising in vitro platform with which to model human development and disease 1–5 . However, lack the connectivity that exists vivo, limits maturation makes integration other circuits control behaviour impossible. Here we show stem cell-derived cortical transplanted into somatosensory cortex of newborn athymic rats develop mature cell types integrate sensory motivation-related circuits. MRI reveals post-transplantation organoid growth across multiple lines animals, whereas single-nucleus profiling shows progression corticogenesis emergence activity-dependent transcriptional programs. Indeed, neurons display more complex morphological, synaptic intrinsic membrane properties than their counterparts, enables discovery defects derived from individuals Timothy syndrome. Anatomical functional tracings receive thalamocortical corticocortical inputs, vivo recordings activity demonstrate these inputs can produce responses cells. Finally, extend axons throughout rat brain optogenetic activation drive reward-seeking behaviour. Thus, engage host We anticipate this approach will be useful for detecting circuit-level phenotypes patient-derived cells cannot otherwise uncovered.

Язык: Английский

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Encoding of danger by parabrachial CGRP neurons

Nature, Год журнала: 2018, Номер 555(7698), С. 617 - 622

Опубликована: Март 1, 2018

Язык: Английский

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Combined Social and Spatial Coding in a Descending Projection from the Prefrontal Cortex

Cell, Год журнала: 2017, Номер 171(7), С. 1663 - 1677.e16

Опубликована: Дек. 1, 2017

Язык: Английский

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Dopamine enhances signal-to-noise ratio in cortical-brainstem encoding of aversive stimuli

Nature, Год журнала: 2018, Номер 563(7731), С. 397 - 401

Опубликована: Ноя. 1, 2018

Язык: Английский

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