Efficient implementation of convolutional neural networks in the data processing of two-photon <i>in vivo</i> imaging

Wang, Yangzhen; Su, Feng; Wang, Shanshan; Yang, Chang; Tian, Yonglu; Yuan, Pingzhi; Liu, Xiaorong; Xiong, Wei; Zhang, Chen

doi:10.1093/bioinformatics/btz055

Cited by 7 publications

(7 citation statements)

References 13 publications

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“…Imaging data were analyzed using ImageJ (National Institutes of Health, Bethesda, MD, USA) and semiautomatically digitized using a custom-made CNN-based program (Wang et al, 2019). Image sequences were first aligned for translational drift in ImageJ.…”

Section: Imaging Data Analysismentioning

confidence: 99%

Restoration of FMRP expression in adult V1 neurons rescues visual deficits in a mouse model of fragile X syndrome

Yang

Tian

et al. 2021

Protein Cell

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Many people affected by fragile X syndrome (FXS) and autism spectrum disorders have sensory processing deficits, such as hypersensitivity to auditory, tactile, and visual stimuli. Like FXS in humans, loss of Fmr1 in rodents also cause sensory, behavioral, and cognitive deficits. However, the neural mechanisms underlying sensory impairment, especially vision impairment, remain unclear. It remains elusive whether the visual processing deficits originate from corrupted inputs, impaired perception in the primary sensory cortex, or altered integration in the higher cortex, and there is no effective treatment. In this study, we used a genetic knockout mouse model (Fmr1KO), in vivo imaging, and behavioral measurements to show that the loss of Fmr1 impaired signal processing in the primary visual cortex (V1). Specifically, Fmr1KO mice showed enhanced responses to low-intensity stimuli but normal responses to high-intensity stimuli. This abnormality was accompanied by enhancements in local network connectivity in V1 microcircuits and increased dendritic complexity of V1 neurons. These effects were ameliorated by the acute application of GABAA receptor activators, which enhanced the activity of inhibitory neurons, or by reintroducing Fmr1 gene expression in knockout V1 neurons in both juvenile and young-adult mice. Overall, V1 plays an important role in the visual abnormalities of Fmr1KO mice and it could be possible to rescue the sensory disturbances in developed FXS and autism patients.

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Section: Imaging Data Analysismentioning

confidence: 99%

Restoration of FMRP expression in adult V1 neurons rescues visual deficits in a mouse model of fragile X syndrome

Yang

Tian

et al. 2021

Protein Cell

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“…2 a. The population neuronal activity in V1 was analyzed using extended constrained nonnegative matrix factorization (CNMF-E) and ImageCN( 16–18 ); 260 spatial components were detected in one of the mice and 320 in the other (Fig. 2 f).…”

Section: Resultsmentioning

confidence: 99%

Cable-free brain imaging with miniature wireless microscopes

Wang

et al. 2022

Preprint

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The invention of the miniaturized microscope has enabled neuroscientists to investigate neural mechanisms in freely moving mice. A lot of efforts have been made to optimize performance of the miniaturized microscope. However, the tethered cables limit the ability of mini-microscope systems to record neural activity from multiple mice simultaneously. Here, we present a wireless mini-microscope (wScope) that enables both real-time remote control and data preview during animal behavior; this design also supports simultaneous recording from up to 8 mice. The wScope has a mass of 2.7 g and a maximum frame rate of 25 Hz at 750 μm by 450 μm field of view with 1.8 μm resolution. We validated the wScopes in video-recording of the cerebral blood flow (CBF) and the activity of neurons in the primary visual cortex (V1) of different mice. The wScope provides a powerful tool for brain imaging of free moving animals, including large primates, in their much larger spaces and more naturalistic environments.

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“…Wang et al [76] proposed a two staged neuron detection pipeline. In the first stage, the raw image stack is first denoised by taking a moving average along temporal axis.…”

Section: Methods Applied To Summary Imagesmentioning

confidence: 99%

Computational Methods for Neuron Segmentation in Two-Photon Calcium Imaging Data: A Survey

Abbas

Masip

2022

Applied Sciences

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Calcium imaging has rapidly become a methodology of choice for real-time in vivo neuron analysis. Its application to large sets of data requires automated tools to annotate and segment cells, allowing scalable image segmentation under reproducible criteria. In this paper, we review and summarize the most recent methods for computational segmentation of calcium imaging. The contributions of the paper are three-fold: we provide an overview of the main algorithms taxonomized in three categories (signal processing, matrix factorization and machine learning-based approaches), we highlight the main advantages and disadvantages of each category and we provide a summary of the performance of the methods that have been tested on public benchmarks (with links to the public code when available).

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Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging

Cited by 7 publications

References 13 publications

Restoration of FMRP expression in adult V1 neurons rescues visual deficits in a mouse model of fragile X syndrome

Restoration of FMRP expression in adult V1 neurons rescues visual deficits in a mouse model of fragile X syndrome

Cable-free brain imaging with miniature wireless microscopes

Computational Methods for Neuron Segmentation in Two-Photon Calcium Imaging Data: A Survey

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