deep-brain-stimulation-with-simultaneous-fmri-in-rodents

Deep Brain Stimulation with Simultaneous fMRI in Rodents

In order to visualize the global and downstream neuronal responses to deep brain stimulation (DBS) at various targets, we have developed a protocol for ...

whole-brain-single-cell-imaging-analysis-intact-neonatal-mouse-brains

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of ...

University of North Carolina

The University of North Carolina at Chapel Hill

High-resolution functional-magnetic-resonance-imaging (fMRI) has been used to study brain functions at increasingly finer scale, but whether fMRI can accurately reflect layer-specific neuronal activities is less well understood. The present study investigated layer-specific cerebral-blood-volume (CBV) fMRI and electrophysiological responses in the rat cortex. CBV fMRI at 40×40 μm in-plane resolution was performed on an 11.7-T scanner. Electrophysiology used a 32-channel electrode array that spanned the entire cortical depth. Graded electrical stimulation was used to study activations in different cortical layers, exploiting the notion that most of the sensory-specific neurons are in layers II-V and most of the nociceptive-specific neurons are in layers V-VI. CBV response was strongest in layer IV of all stimulus amplitudes. Current source density analysis showed strong sink currents at cortical layers IV and VI. Multi-unit activities mainly appeared at layers IV-VI and peaked at layer V. Although our measures showed scaled activation profiles during modulation of stimulus amplitude and failed to detect specific recruitment at layers V and VI during noxious electrical stimuli, there appears to be discordance between CBV fMRI and electrophysiological peak responses, suggesting neurovascular uncoupling at laminar resolution. The technique implemented in the present study offers a means to investigate intracortical neurovascular function in the normal and diseased animal models at laminar resolution.

Ultra high-resolution fMRI and electrophysiology of the rat primary somatosensory cortex.

Blood flow (BF) in many tissues is stable during significant fluctuations in systemic arterial blood pressure or perfusion pressure under normal conditions. The regulatory mechanisms responsible for this non-passive BF behavior include both local and neural control mechanisms. This study evaluated cerebral BF (CBF), retinal BF (RBF) and choroidal BF (ChBF) responses to acute blood pressure increases in rats using magnetic resonance imaging (MRI). A transient increase in blood pressure inside the MRI scanner was achieved by mechanically inflating a balloon catheter to occlude the descending aorta near the diaphragm. We verified the rat model of mechanical occlusion and MRI approach by first measuring blood-flow regulatory responses to changing BP in the brain under normoxia and hypercapnia where the phenomenon is well documented. Retinal and choroidal blood-flow responses to transient increased arterial pressure were then investigated. In response to an acute increase in blood pressure, RBF exhibited autoregulatory behavior and ChBF exhibited baroregulation similar to that seen in the cerebral circulation. This approach may prove useful to investigate retinal and choroidal vascular dysregulation in rat models of retinal diseases with suspected vascular etiology.

MRI study of cerebral, retinal and choroidal blood flow responses to acute hypertension.

Vascular pathology is a major feature of Alzheimer's disease (AD) and other dementias. We recently showed that chronic administration of the target-of-rapamycin (TOR) inhibitor rapamycin, which extends lifespan and delays aging, halts the progression of AD-like disease in transgenic human (h)APP mice modeling AD when administered before disease onset. Here we demonstrate that chronic reduction of TOR activity by rapamycin treatment started after disease onset restored cerebral blood flow (CBF) and brain vascular density, reduced cerebral amyloid angiopathy and microhemorrhages, decreased amyloid burden, and improved cognitive function in symptomatic hAPP (AD) mice. Like acetylcholine (ACh), a potent vasodilator, acute rapamycin treatment induced the phosphorylation of endothelial nitric oxide (NO) synthase (eNOS) and NO release in brain endothelium. Administration of the NOS inhibitor L-NG-Nitroarginine methyl ester reversed vasodilation as well as the protective effects of rapamycin on CBF and vasculature integrity, indicating that rapamycin preserves vascular density and CBF in AD mouse brains through NOS activation. Taken together, our data suggest that chronic reduction of TOR activity by rapamycin blocked the progression of AD-like cognitive and histopathological deficits by preserving brain vascular integrity and function. Drugs that inhibit the TOR pathway may have promise as a therapy for AD and possibly for vascular dementias.

Chronic rapamycin restores brain vascular integrity and function through NO synthase activation and improves memory in symptomatic mice modeling Alzheimer's disease.

Deep brain stimulation (DBS) represents a widely used therapeutic tool for the symptomatic treatment of movement disorders, most commonly Parkinson's disease (PD). High frequency stimulation at both the subthalamic nucleus (STN) and internal globus pallidus (GPi) has been used with great success for the symptomatic treatment of PD, although the therapeutic mechanisms of action remain elusive. To better understand how DBS at these target sites modulates neural circuitry, the present study used functional blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) to map global brain responses to DBS at the STN and GPi of the rat. Robust activation centered in the ipsilateral motor cortex was observed during high frequency stimulation at either target site, with peak responses observed at a stimulation frequency of 100Hz. Of note, frequency tuning curves were generated, demonstrating that cortical activation was maximal at clinically-relevant stimulation frequencies. Divergent responses to stimulation were noted in the contralateral hemisphere, with strong cortical and striatal negative BOLD signal during stimulation of the GPi, but not STN. The frequency-dependence of the observed motor cortex activation at both targets suggests a relationship with the therapeutic effects of STN and GPi DBS, with both DBS targets being functionally connected with motor cortex at therapeutic stimulation frequencies.

Functional MRI reveals frequency-dependent responses during deep brain stimulation at the subthalamic nucleus or internal globus pallidus.

Abstract Deep brain stimulation (DBS) targeting the subthalamic nucleus (STN) represents a powerful clinical tool for the alleviation of many motor symptoms that are associated with Parkinson's disease. Despite its extensive use, the underlying therapeutic mechanisms of STN-DBS remain poorly understood. In the present review, we integrate and discuss recent literature examining the network effects of STN-DBS for Parkinson's disease, placing emphasis on neuroimaging findings, including functional magnetic resonance imaging, positron emission tomography, and single-photon emission computed tomography. These techniques enable the noninvasive detection of brain regions that are modulated by DBS on a whole-brain scale, representing a key experimental strength given the diffuse and far-reaching effects of electrical field stimulation. By examining these data in the context of multiple hypotheses of DBS action, generally developed through clinical and physiological observations, we define a multitude of consistencies and inconsistencies in the developing literature of this rapidly moving field.

Neural Circuit Modulation During Deep Brain Stimulation at the Subthalamic Nucleus for Parkinson's Disease: What Have We Learned from Neuroimaging Studies?

Functional magnetic resonance imaging (fMRI) of deep brain stimulation (DBS) has potentials to reveal neuroanatomical connectivity of a specific brain region in vivo.

fMRI of Deep Brain Stimulation at the Rat Ventral Posteromedial Thalamus.

Animal whole-brain functional magnetic resonance imaging (fMRI) provides a non-invasive window into brain activity. A collection of associated methods aims to replicate observations made in humans and to identify the mechanisms underlying the distributed neuronal activity in the healthy and disordered brain. Animal fMRI studies have developed rapidly over the past years, fueled by the development of resting-state fMRI connectivity and genetically encoded neuromodulatory tools. Yet, comparisons between sites remain hampered by lack of standardization. Recently, we highlighted that mouse resting-state functional connectivity converges across centers, although large discrepancies in sensitivity and specificity remained. Here, we explore past and present trends within the animal fMRI community and highlight critical aspects in study design, data acquisition, and post-processing operations, that may affect the results and influence the comparability between studies. We also suggest practices aimed to promote the adoption of standards within the community and improve between-lab reproducibility. The implementation of standardized animal neuroimaging protocols will facilitate animal population imaging efforts as well as meta-analysis and replication studies, the gold standards in evidence-based science.

Animal Functional Magnetic Resonance Imaging: Trends and Path Toward Standardization.

Accurate removal of magnetic resonance imaging (MRI) signal outside the brain, a.k.a., skull stripping, is a key step in the brain image pre-processing pipelines. In rodents, this is mostly achieved by manually editing a brain mask, which is time-consuming and operator dependent. Automating this step is particularly challenging in rodents as compared to humans, because of differences in brain/scalp tissue geometry, image resolution with respect to brain-scalp distance, and tissue contrast around the skull. In this study, we proposed a deep-learning-based framework, U-Net, to automatically identify the rodent brain boundaries in MR images. The U-Net method is robust against inter-subject variability and eliminates operator dependence. To benchmark the efficiency of this method, we trained and validated our model using both in-house collected and publicly available datasets. In comparison to current state-of-the-art methods, our approach achieved superior averaged Dice similarity coefficient to ground truth T2-weighted rapid acquisition with relaxation enhancement and T2-weighted echo planar imaging data in both rats and mice (all  < 0.05), demonstrating robust performance of our approach across various MRI protocols.

Automatic Skull Stripping of Rat and Mouse Brain MRI Data Using U-Net.

The vascular contributions of neurotransmitters to the hemodynamic response are gaining more attention in neuroimaging studies, as many neurotransmitters are vasomodulatory. To date, well-established electrochemical techniques that detect neurotransmission in high magnetic field environments are limited. Here, we propose an experimental setting enabling simultaneous fast-scan cyclic voltammetry (FSCV) and blood oxygenation level-dependent functional magnetic imaging (BOLD fMRI) to measure both local tissue oxygen and dopamine responses, and global BOLD changes, respectively. By using MR-compatible materials and the proposed data acquisition schemes, FSCV detected physiological analyte concentrations with high temporal resolution and spatial specificity inside of a 9.4 T MRI bore. We found that tissue oxygen and BOLD correlate strongly, and brain regions that encode dopamine amplitude differences can be identified via modeling simultaneously acquired dopamine FSCV and BOLD fMRI time-courses. This technique provides complementary neurochemical and hemodynamic information and expands the scope of studying the influence of local neurotransmitter release over the entire brain.

Simultaneous fMRI and fast-scan cyclic voltammetry bridges evoked oxygen and neurotransmitter dynamics across spatiotemporal scales.

Brain extraction is a critical pre-processing step in brain magnetic resonance imaging (MRI) analytical pipelines. In rodents, this is often achieved by manually editing brain masks slice-by-slice, a time-consuming task where workloads increase with higher spatial resolution datasets. We recently demonstrated successful automatic brain extraction via a deep-learning-based framework, U-Net, using 2D convolutions. However, such an approach cannot make use of the rich 3D spatial-context information from volumetric MRI data. In this study, we advanced our previously proposed U-Net architecture by replacing all 2D operations with their 3D counterparts and created a 3D U-Net framework. We trained and validated our model using a recently released CAMRI rat brain database acquired at isotropic spatial resolution, including T2-weighted turbo-spin-echo structural MRI and T2*-weighted echo-planar-imaging functional MRI. The performance of our 3D U-Net model was compared with existing rodent brain extraction tools, including Rapid Automatic Tissue Segmentation, Pulse-Coupled Neural Network, SHape descriptor selected External Regions after Morphologically filtering, and our previously proposed 2D U-Net model. 3D U-Net demonstrated superior performance in Dice, Jaccard, center-of-mass distance, Hausdorff distance, and sensitivity. Additionally, we demonstrated the reliability of 3D U-Net under various noise levels, evaluated the optimal training sample sizes, and disseminated all source codes publicly, with a hope that this approach will benefit rodent MRI research community.  We proposed a deep-learning-based framework to automatically identify the rodent brain boundaries in MRI. With a fully 3D convolutional network model, 3D U-Net, our proposed method demonstrated improved performance compared to current automatic brain extraction methods, as shown in several qualitative metrics (Dice, Jaccard, PPV, SEN, and Hausdorff). We trust that this tool will avoid human bias and streamline pre-processing steps during 3D high resolution rodent brain MRI data analysis. The software developed herein has been disseminated freely to the community.

3D U-Net Improves Automatic Brain Extraction for Isotropic Rat Brain Magnetic Resonance Imaging Data.

Coupling of hemodynamic responses to neuronal activity is the foundation of several functional neuroimaging techniques. Here, we provide three fiber-photometry approaches to simultaneously measure neuronal and vascular signals in the rodent brain using a spectrometer-based system. Two out of these three approaches allow the removal of hemoglobin (Hb)-absorption artifacts and restore the underlying neuronal activity. This technique is applicable to different fluorescent sensors and provides a more accurate measurement of hemodynamic response function in any location of the rodent brain. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).

ArticleTotal : 2	Year
Publication title Cited by 21	2014
Publication title Cited by 2	2022

Article	Year
Ultra high-resolution fMRI and electrophysiology of the rat primary somatosensory cortex. NeuroImage\| PubMed ID: 23384528	2013
MRI study of cerebral, retinal and choroidal blood flow responses to acute hypertension. Experimental eye research\| PubMed ID: 23623996	2013
Chronic rapamycin restores brain vascular integrity and function through NO synthase activation and improves memory in symptomatic mice modeling Alzheimer's disease. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism\| PubMed ID: 23801246	2013
Functional MRI reveals frequency-dependent responses during deep brain stimulation at the subthalamic nucleus or internal globus pallidus. NeuroImage\| PubMed ID: 23988274	2014
Neural Circuit Modulation During Deep Brain Stimulation at the Subthalamic Nucleus for Parkinson's Disease: What Have We Learned from Neuroimaging Studies? Brain connectivity\| PubMed ID: 24147633	2013
fMRI of Deep Brain Stimulation at the Rat Ventral Posteromedial Thalamus. Brain stimulation\| PubMed ID: 24309153	2013
Animal Functional Magnetic Resonance Imaging: Trends and Path Toward Standardization. Frontiers in neuroinformatics\| PubMed ID: 32038217	2019
Automatic Skull Stripping of Rat and Mouse Brain MRI Data Using U-Net. Frontiers in neuroscience\| PubMed ID: 33117118	2020
Simultaneous fMRI and fast-scan cyclic voltammetry bridges evoked oxygen and neurotransmitter dynamics across spatiotemporal scales. NeuroImage\| PubMed ID: 34624504	2021
3D U-Net Improves Automatic Brain Extraction for Isotropic Rat Brain Magnetic Resonance Imaging Data. Frontiers in neuroscience\| PubMed ID: 34975392	2021
Simultaneous recording of neuronal and vascular activity in the rodent brain using fiber-photometry. STAR protocols\| PubMed ID: 35776651	2022

Yen-Yu Ian Shih

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