MesoNet allows automated scaling and segmentation of mouse mesoscale cortical maps using machine learning

Xiao, Dongsheng; Forys, Brandon J; Vanni, Matthieu P.; Murphy, Timothy H.

doi:10.1038/s41467-021-26255-2

Cited by 36 publications

(23 citation statements)

References 72 publications

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“…First, a flattened cortical map was generated from the reference atlas, and the map was manually trimmed to fit our imaging data by removing a fraction of the most posterior and lateral regions in the neocortex. Such an operation is commonly used in previous studies 22 , 69 , 74 . We then merged small anatomy regions in the map and got the final reference regional map with nine brain regions, including the primary motor cortex (MOs), the secondary motor cortex (Mop), the somatosensory cortex, barrel field (SSb), the somatosensory cortex, upper limb (SSu), the somatosensory cortex, lower limb (SSl), the primary visual cortex (VISp), the association visual cortex (VISs), the dorsal retrosplenial cortex (RSPd), and the lateral retrosplenial cortex (RSPl).…”

Section: Methodsmentioning

confidence: 99%

REM sleep is associated with distinct global cortical dynamics and controlled by occipital cortex

et al. 2022

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The cerebral cortex is spontaneously active during sleep, yet it is unclear how this global cortical activity is spatiotemporally organized, and whether such activity not only reflects sleep states but also contributes to sleep state switching. Here we report that cortex-wide calcium imaging in mice revealed distinct sleep stage-dependent spatiotemporal patterns of global cortical activity, and modulation of such patterns could regulate sleep state switching. In particular, elevated activation in the occipital cortical regions (including the retrosplenial cortex and visual areas) became dominant during rapid-eye-movement (REM) sleep. Furthermore, such pontogeniculooccipital (PGO) wave-like activity was associated with transitions to REM sleep, and optogenetic inhibition of occipital activity strongly promoted deep sleep by suppressing the NREM-to-REM transition. Thus, whereas subcortical networks are critical for initiating and maintaining sleep and wakefulness states, distinct global cortical activity also plays an active role in controlling sleep states.

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Section: Methodsmentioning

confidence: 99%

REM sleep is associated with distinct global cortical dynamics and controlled by occipital cortex

et al. 2022

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“…We recommend generating this mask using the reference frame. Although the automated generation of a brain mask from mesoscale imaging data has been described [48], we find user-drawn masks to be more robust to image artifacts. Inputs are summarized in Table 1 .…”

Section: Resultsmentioning

confidence: 98%

Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type

O’Connor

Mandino

Shen

et al. 2022

Preprint

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To improve bench-to-bedside translation, it is integral that knowledge flow bidirectionally from - animal models to humans, and vice versa. This will be facilitated by the application of common analytical frameworks, as well as open software and data sharing practices. To these ends, we share a new pipeline (and test dataset) for the preprocessing of wide-field optical fluorescence imaging data - an emerging mode applicable in animal models - as well as results from a functional connectivity and graph theory analysis of these data that is inspired by recent work in the human neuroimaging field. The approach is demonstrated using a dataset comprised of two test-cases: (1) data from animals imaged during awake and anesthetized conditions with excitatory neurons labeled, and (2) data from awake animals with different genetically encoded fluorescent labels that target either excitatory neurons or inhibitory interneuron subtypes. Both seed-based connectivity and graph theory measures (global efficiency, transitivity, modularity, and characteristic path-length) are shown to be useful in quantifying differences between consciousness states and cell populations. The graph theory measures are shown to be capable of characterizing the dependence on canonical network and frequency band (infra-slow versus delta). Both consciousness state and cell population show widespread effects on canonical network connectivity with variable frequency band dependence. Effects of anesthesia are also revealed across graph theory measures (particularly in the delta band). Differences between excitatory neurons and inhibitory interneurons are observed, with somatostatin expressing inhibitory interneurons emerge as notably dissimilar from parvalbumin and vasoactive polypeptide expressing cells. We recommend this pipeline as a step in harmonization between preclinical and human research enabling comparison of results across both scales and species.

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“…All GCaMP responses were movement and hemodynamic artifact corrected by subtracting changes in green reflectance signals from observed green epi-fluorescence (Vanni et al, 2017) and expressed as percentages relative to baseline responses (F-F 0 /F 0 )*100 where F 0 is the baseline from the start of the trial to water reward delivery. For region-based analysis, the brain-to-atlas approach in MesoNet (Xiao et al, 2021) was used to register cortical images to a common atlas using predicted cortical landmarks to determine regions of interest (ROIs). A 5 x 5 pixel region centered in each ROI was used for examination of peak amplitude and baseline standard deviation.…”

Section: Methodsmentioning

confidence: 99%

Longitudinal assessment of water-reaching reveals altered cortical activity and fine motor coordination defects in a Huntington Disease model

Wang

Sepers

Xiao

et al. 2022

Preprint

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Huntington Disease (HD), caused by dominantly inherited expansions of a CAG repeat results in characteristic motor dysfunction. Although gross motor and balance defects have been extensively characterized in multiple HD mouse models using tasks such as rotarod, beam walking and gait analysis, little is known about forelimb deficits. Here we use a high-throughput alternating reward/non-reward water-reaching task conducted daily over ~2 months to simultaneously monitor forelimb impairment and mesoscale cortical changes in GCaMP activity, comparing female zQ175 (HD) and wildtype (WT) littermate mice, starting at ~5.5 months of age. Behavioral analysis of the water-reaching task reveals that HD mice, despite learning the water-reaching task as proficiently as WT mice, take longer to learn the alternating event sequence. Although WT mice displayed no significant changes in cortical activity and reaching trajectory throughout the testing period, HD mice exhibited an increase in cortical activity - especially in the secondary motor and retrosplenial cortices - over time, as well as longer and more variable reaching trajectories by ~7 months of age. HD mice also experienced a progressive reduction in successful performance rates. Tapered beam and rotarod tests before and/or after water-reaching assessment confirmed these early and manifest stages of HD characterized by the absence and presence of failed water-reaching trials, respectively. Reduced DARPP-32 (marker for striatal medium spiny neurons) expression in HD mice further confirmed disease pathology. The water-reaching task can be used to inform HD and potentially other movement disorder onset, therapeutic intervention windows and test drug efficacy.

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MesoNet allows automated scaling and segmentation of mouse mesoscale cortical maps using machine learning

Cited by 36 publications

References 72 publications

REM sleep is associated with distinct global cortical dynamics and controlled by occipital cortex

REM sleep is associated with distinct global cortical dynamics and controlled by occipital cortex

Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type

Longitudinal assessment of water-reaching reveals altered cortical activity and fine motor coordination defects in a Huntington Disease model

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