Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT

Johnston, Kevin G.; Grieco, Steven F.; Zhang, Hai; Jin, Suoqin; Xu, Xiangmin; Nie, Qing

doi:10.1016/j.crmeth.2022.100207

Cited by 6 publications

(2 citation statements)

References 27 publications

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“…While care must be taken to align the imaging FOV across sessions, there are tools to perform flexible alignment of cellular imaging datasets acquired across sessions. 102,103 Further, image-forming optical methods present an opportunity to perform post-hoc anatomical, histological, or in-situ sequencing analysis of physiologically characterized cells, providing an additional dimension and degree of specificity. [104][105][106] The spatial and temporal resolution, FOV, and tissue depth penetration of imaging-forming techniques depend on the specifics of their optical system (especially on magnification and the numerical aperture, NA), scan technology (line-, raster-, or random-access scanning), and on whether single-photon or multiphoton excitation is used.…”

Section: Strengths and Limitations Of Optical Measurementsmentioning

confidence: 99%

Linking brain activity across scales with simultaneous opto- and electrophysiology

Lewis,

Hoffmann,

Helmchen

2023

Neurophoton.

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The brain enables adaptive behavior via the dynamic coordination of diverse neuronal signals across spatial and temporal scales: from fast action potential patterns in microcircuits to slower patterns of distributed activity in brain-wide networks. Understanding principles of multiscale dynamics requires simultaneous monitoring of signals in multiple, distributed network nodes. Combining optical and electrical recordings of brain activity is promising for collecting data across multiple scales and can reveal aspects of coordinated dynamics invisible to standard, singlemodality approaches. We review recent progress in combining opto-and electrophysiology, focusing on mouse studies that shed new light on the function of single neurons by embedding their activity in the context of brain-wide activity patterns. Optical and electrical readouts can be tailored to desired scales to tackle specific questions. For example, fast dynamics in single cells or local populations recorded with multi-electrode arrays can be related to simultaneously acquired optical signals that report activity in specified subpopulations of neurons, in non-neuronal cells, or in neuromodulatory pathways. Conversely, two-photon imaging can be used to densely monitor activity in local circuits while sampling electrical activity in distant brain areas at the same time. The refinement of combined approaches will continue to reveal previously inaccessible and under-appreciated aspects of coordinated brain activity.

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Section: Strengths and Limitations Of Optical Measurementsmentioning

confidence: 99%

Linking brain activity across scales with simultaneous opto- and electrophysiology

Lewis,

Hoffmann,

Helmchen

2023

Neurophoton.

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show abstract

“…We next compared CaliAli's performance with that of other neural tracking algorithms in three scenarios common to Ca 2+ imaging experiments: (1) low overlap of neurons with active populations remaining consistent across sessions (Fig. 2d), (2) high overlap of neurons (Fig. 2e), and (3) remapping of neuronal population activity (Fig.…”

Section: )mentioning

confidence: 99%

CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging

Kano

Wang

Srinivasan

et al. 2023

Preprint

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Neuron-tracking algorithms exhibit suboptimal performance in calcium imaging when the same neurons are not consistently detected, as unmatched features hinder inter-session alignment. CaliAli addresses this issue by employing an alignment-before-extraction strategy that incorporates vasculature information to improve the detectability of weak signals and maximize the number of trackable neurons. By excelling in neural remapping and high spatial overlap scenarios, CaliAli paves the way toward further understanding long-term neural network dynamics.

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Time-Varying ℓ ₀ Optimization for Spike Inference from Multi-Trial Calcium Recordings

Shen,

Du,

Johnston

et al. 2024

Data Science in Science

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Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT

Cited by 6 publications

References 27 publications

Linking brain activity across scales with simultaneous opto- and electrophysiology

Linking brain activity across scales with simultaneous opto- and electrophysiology

CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging

Time-Varying ℓ ₀ Optimization for Spike Inference from Multi-Trial Calcium Recordings

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Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT

Cited by 6 publications

References 27 publications

Linking brain activity across scales with simultaneous opto- and electrophysiology

Linking brain activity across scales with simultaneous opto- and electrophysiology

CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging

Time-Varying ℓ 0 Optimization for Spike Inference from Multi-Trial Calcium Recordings

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Product

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Time-Varying ℓ ₀ Optimization for Spike Inference from Multi-Trial Calcium Recordings