Fluorescence imaging of large-scale neural ensemble dynamics

Kim, Tony Hyun; Schnitzer, Mark J.

doi:10.1016/j.cell.2021.12.007

Cited by 95 publications

(67 citation statements)

References 266 publications

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“…These are molecular probes that rapidly and reversibly emit fluorescent signal in response to action potentials. In particular, genetically encoded calcium indicators have been used extensively to image large populations of neuronal activity in behaving animals when combined with florescence-detecting tools such as fiber optic recording, widefield microscopy, confocal microscopy, two-photon microscopy, or headmounted miniature microscopes (61,64). Similarly, fluorescent neurotransmitter indicators (65) are also available to detect specific neurotransmitter release, such as glutamate (66), acetylcholine (67), or γ-aminobutyric acid (68) and monitor the response of neuronal populations.…”

Section: Box 1 Engram Cells and Place Cellsmentioning

confidence: 99%

Understanding the physical basis of memory: Molecular mechanisms of the engram

Ryan

2022

Journal of Biological Chemistry

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Section: Box 1 Engram Cells and Place Cellsmentioning

confidence: 99%

Understanding the physical basis of memory: Molecular mechanisms of the engram

Ryan

2022

Journal of Biological Chemistry

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“…Compared with electrophysiological methods, optical imaging in vivo is typically less invasive and could record several brain areas up to millimeter-level field of view (FOV) at cellular resolution. 1 , 2 Animal surgeries, such as cranial window, thinned skull, or crystal skull 3 , 4 provide the optical imaging window for one-photon imaging to achieve single-cell resolution in the superficial cortex, such as layer 2/3. Optical neural imaging has thus been used to investigate neural structure change, 5 , 6 brain state alteration, 7 and information flow while the animal performs a specific task.…”

Section: Introductionmentioning

confidence: 99%

“…To date, multiple imaging modalities are capable of mesoscale recording with single-cell resolution and millimeter-level FOV, such as single-photon widefield microscopy, 3 , 17 multi-photon microscopy, 18 , 19 light-field microscopy, 20 , 21 and light-sheet microscopy. 22 A recent review 2 has described the mesoscale imaging techniques and related animal models in detail, which also points out its increasing importance in neuroscience. While the challenges and opportunities brought by the large-scale mesoscale data have been gradually realized by the community, 2 there is still not a comprehensive review about the existing mesoscale analysis methods, remaining problems, and potential future directions.…”

Section: Introductionmentioning

confidence: 99%

“… 22 A recent review 2 has described the mesoscale imaging techniques and related animal models in detail, which also points out its increasing importance in neuroscience. While the challenges and opportunities brought by the large-scale mesoscale data have been gradually realized by the community, 2 there is still not a comprehensive review about the existing mesoscale analysis methods, remaining problems, and potential future directions. Here, we intended to provide a general data analysis pipeline for cellular level mesoscale neural imaging without focusing on any specific imaging modality.…”

Section: Introductionmentioning

confidence: 99%

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Review on data analysis methods for mesoscale neural imaging in vivo

Cai

Dai

2022

Neurophoton.

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. Significance: Mesoscale neural imaging in vivo has gained extreme popularity in neuroscience for its capacity of recording large-scale neurons in action. Optical imaging with single-cell resolution and millimeter-level field of view in vivo has been providing an accumulated database of neuron-behavior correspondence. Meanwhile, optical detection of neuron signals is easily contaminated by noises, background, crosstalk, and motion artifacts, while neural-level signal processing and network-level coordinate are extremely complicated, leading to laborious and challenging signal processing demands. The existing data analysis procedure remains unstandardized, which could be daunting to neophytes or neuroscientists without computational background. Aim: We hope to provide a general data analysis pipeline of mesoscale neural imaging shared between imaging modalities and systems. Approach: We divide the pipeline into two main stages. The first stage focuses on extracting high-fidelity neural responses at single-cell level from raw images, including motion registration, image denoising, neuron segmentation, and signal extraction. The second stage focuses on data mining, including neural functional mapping, clustering, and brain-wide network deduction. Results: Here, we introduce the general pipeline of processing the mesoscale neural images. We explain the principles of these procedures and compare different approaches and their application scopes with detailed discussions about the shortcomings and remaining challenges. Conclusions: There are great challenges and opportunities brought by the large-scale mesoscale data, such as the balance between fidelity and efficiency, increasing computational load, and neural network interpretability. We believe that global circuits on single-neuron level will be more extensively explored in the future.

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“…The focus of this minireview is not to describe in detail diverse Ca 2+ imaging techniques as excellent, comprehensive reviews are already available ( Werner et al, 2019 ; Broussard and Petreanu, 2021 ; Wang et al, 2021 ; Grienberger et al, 2022 ; Kim and Schnitzer, 2022 ; Lake and Higley, 2022 ). Instead, we discuss studies using some of these techniques to monitor the activity of neurons, astrocytes, and mitochondria in HD models ( Table 1 ).…”

Section: Introductionmentioning

confidence: 99%

Calcium imaging: A versatile tool to examine Huntington’s disease mechanisms and progression

Barry

Peng²,

Levine³

et al. 2022

Front. Neurosci.

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Huntington’s disease (HD) is a fatal, hereditary neurodegenerative disorder that causes chorea, cognitive deficits, and psychiatric symptoms. It is characterized by accumulation of mutant Htt protein, which primarily impacts striatal medium-sized spiny neurons (MSNs), as well as cortical pyramidal neurons (CPNs), causing synapse loss and eventually cell death. Perturbed Ca2+ homeostasis is believed to play a major role in HD, as altered Ca2+ homeostasis often precedes striatal dysfunction and manifestation of HD symptoms. In addition, dysregulation of Ca2+ can cause morphological and functional changes in MSNs and CPNs. Therefore, Ca2+ imaging techniques have the potential of visualizing changes in Ca2+ dynamics and neuronal activity in HD animal models. This minireview focuses on studies using diverse Ca2+ imaging techniques, including two-photon microscopy, fiber photometry, and miniscopes, in combination of Ca2+ indicators to monitor activity of neurons in HD models as the disease progresses. We then discuss the future applications of Ca2+ imaging to visualize disease mechanisms and alterations associated with HD, as well as studies showing how, as a proof-of-concept, Ca2+imaging using miniscopes in freely-behaving animals can help elucidate the differential role of direct and indirect pathway MSNs in HD symptoms.

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Fluorescence imaging of large-scale neural ensemble dynamics

Cited by 95 publications

References 266 publications

Understanding the physical basis of memory: Molecular mechanisms of the engram

Understanding the physical basis of memory: Molecular mechanisms of the engram

Review on data analysis methods for mesoscale neural imaging in vivo

Calcium imaging: A versatile tool to examine Huntington’s disease mechanisms and progression

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