Neuroimaging

Source: Provenzano, G., et al. Immunohistochemical Visualization of Hippocampal Neuron Activity After Spatial Learning in a Mouse Model of Neurodevelopmental Disorders. J. Vis. Exp. (2015)This video demonstrates immunohistochemical imaging to visualize hippocampal neuronal activation. Stained brain sections reveal darker regions under a bright-field microscope, indicating activated neurons.

Source: Galenchik-Chan, A., et al. Functional Magnetic Resonance Imaging (fMRI) of the Visual Cortex with Wide-View Retinotopic Stimulation. J. Vis. Exp. (2023). The video demonstrates functional magnetic resonance imaging (fMRI) of the visual cortex to map activity based on blood oxygenation levels. Structural MRI images are acquired as anatomical references, followed by fMRI scans. Visual stimuli are displayed to activate retinotopic neurons in the visual cortex. The increased energy demand...

Source: Wang, J., et al. Visualizing the Calcitonin Gene-Related Peptide Immunoreactive Innervation of the Rat Cranial Dura Mater with Immunofluorescence and Neural Tracing. J. Vis. Exp. (2021). This video demonstrates a method to trace the origins of sensory neurons in the dura mater using fluorescence microscopy. A retrograde tracer is introduced into the exposed dura mater of an anesthetized rat. The tracer is taken up by sensory neuronal axons and travels retrogradely to their cell bodies...

Source: Sabado, V., et al., Nagoshi, E. Single-cell Resolution Fluorescence Live Imaging of Drosophila Circadian Clocks in Larval Brain Culture. J. Vis. Exp. (2018). This video demonstrates the procedure to embed the Drosophila brain in a fibrin matrix, followed by time-lapse fluorescence imaging of circadian clock neurons to analyze rhythmic activity synchronized with light/dark cycles.

Source: Bancroft, E. A., et al. Quantifying Spontaneous Ca2+ Fluxes and their Downstream Effects in Primary Mouse Midbrain Neurons. J. Vis. Exp. (2020) This video demonstrates the real-time visualization of calcium influx in ventral midbrain neurons derived from mouse embryos. Using a viral vector to express a calcium indicator, the neurons are imaged under a confocal microscope to track changes in fluorescence intensity during spontaneous and neurotransmitter-induced calcium activity.

Source: Calvo-Rodríguez, et al. Fluorescence and Bioluminescence Imaging of Subcellular Ca2+ in Aged Hippocampal Neurons. J. Vis. Exp. (2015). This video demonstrates the use of fluorescence imaging to measure cytosolic calcium levels in short-term and long-term rat hippocampal cultures. By comparing young and aged neurons, it highlights how increased L-type voltage-gated calcium channel density and prolonged activation in aged neurons result in calcium overloading, a hallmark of neuronal aging.

Source: Reindl, V., et al. Conducting Hyperscanning Experiments with Functional Near-Infrared Spectroscopy. J. Vis. Exp. (2019) This video demonstrates the use of functional near-infrared spectroscopy (fNIRS) to measure brain activity during social interactions. Participants engage in a coordinated task that increases activity in the prefrontal cortex, a region critical for social behavior, while the system detects changes in light absorption due to blood oxygenation. By analyzing the synchrony...

Begin with a patient diagnosed with cerebral aneurysms, a condition where blood vessels in the brain bulge and fill with blood.Secure the patient’s head inside the head coil of an MRI machine. Initiate imaging. The system generates a strong magnetic field, aligning protons in the brain tissue along its direction. Initiate the magnetization-prepared rapid gradient echo or MPRAGE sequence by applying an inversion radiofrequency pulse, flipping the protons’ alignment opposite to the magnetic field.

A traumatic brain injury, or TBI, impairs blood flow to the impacted regions and disrupts the activity of dopaminergic neurons.To investigate TBI-associated disruptions, begin by intravenously injecting a lipophilic radioactive tracer into a patient.The tracer travels through the cerebral vessels and diffuses into cells of the cortical and subcortical brain tissue.Perform single photon emission computed tomography, or SPECT, to detect the tracer-emitted radiation. The resulting signal intensity...

Source: Wiegreffe, C., et. al., Time-lapse Confocal Imaging of Migrating Neurons in Organotypic Slice Culture of Embryonic Mouse Brain Using In Utero Electroporation. J. Vis. Exp. (2017) This video demonstrates time-lapse confocal microscopy to observe cortical neuron radial migration from the subventricular zone to the cortical plate via radial glial scaffolds in transduced mouse embryonic brain slices.

Position a human participant’s head within the head coil of a functional magnetic resonance imaging, or fMRI, system.Employ vascular space occupancy or VASO, a technique to measure changes in cerebral blood volume, or CBV, the blood volume within the brain.Begin by applying an inversion recovery pulse to suppress signals from blood, allowing only signals from the surrounding tissue within the region to be detected.Next, use MRI-compatible earbuds to deliver auditory stimuli.The stimuli reach...

Source: Schott, J. T., et al. Preparation of Rat Oligodendrocyte Progenitor Cultures and Quantification of Oligodendrogenesis Using Dual-infrared Fluorescence Scanning. J. Vis. Exp. (2016). This video demonstrates the use of dual fluorescence imaging to evaluate the differentiation of oligodendrocytes from precursor cells (OPCs) isolated from a rat pup brain. The process includes fixing the cells, labeling specific markers with primary and fluorophore-conjugated secondary antibodies, and...

Source: Upputuri, P. K., et al. A High-performance Compact Photoacoustic Tomography System for In Vivo Small-animal Brain Imaging. J. Vis. Exp. (2017)This video demonstrates a protocol for in vivo non-invasive rat brain imaging using photoacoustic tomography, showcasing the preparation, imaging system setup, and data acquisition to reconstruct 2D brain images for visualizing vascular structures and neurovascular health.

Source: Shimojo, H., et al. Real-time Bioluminescence Imaging of Notch Signaling Dynamics during Murine Neurogenesis. J. Vis. Exp. (2019)In this video, cortical slice cultures from transgenic mouse embryos are used to monitor gene expression through Three-dimensional imaging. Bioluminescence, fluorescence, and bright-field images are used to visualize real-time gene expression during neuronal differentiation within the native tissue.

Source: Jamadar, S. et. al. Radiotracer Administration for High Temporal Resolution Positron Emission Tomography of the Human Brain: Application to FDG-fPET. J. Vis. Exp. (2019)This video demonstrates the quantification of brain glucose metabolism using positron emission tomography (PET). The participant is infused with the tracer F-18 fluorodeoxyglucose (FDG) during scanning. FDG accumulates in active neurons and emits positrons upon F-18 decay. These positrons interact with electrons,...

Source: Delalande, J., et.al. Dual Labeling of Neural Crest Cells and Blood Vessels Within Chicken Embryos Using ChickGFP Neural Tube Grafting and Carbocyanine Dye DiI Injection. J. Vis. Exp. (2015)This video demonstrates the transplantation of a GFP-labeled donor neural tube from a stage-matched transgenic chicken embryo into a recipient embryo at the level of somites one to seven, followed by vascular labeling using a lipophilic fluorescent dye. The combined approach allows for direct...

Source: Zheng, W. et. al., Diffusion Tensor Magnetic Resonance Imaging in Chronic Spinal Cord Compression. J. Vis. Exp. (2019)This video demonstrates diffusion tensor imaging in assessing chronic spinal cord compression. By analyzing water diffusion patterns, fractional anisotropy, and apparent diffusion coefficient values, the findings reveal axonal damage in compressed regions. The findings provide critical insights into spinal cord pathology and structural integrity.

Source: Fowler, B. E., et al. In vivo Calcium Imaging of Mouse Geniculate Ganglion Neuron Responses to Taste Stimuli. J. Vis. Exp. (2021) This video demonstrates a protocol for delivering tastants to the surgically exposed geniculate ganglion in an anesthetized mouse and using GCaMP fluorescence with epifluorescent microscopy to visualize real-time neuronal responses, aiding studies on peripheral taste signal processing.

Source: Blanc, J., et al. Functional Magnetic Resonance Spectroscopy at 7 T in the Rat Barrel Cortex During Whisker Activation. J. Vis. Exp. (2019)This video demonstrates the method of analyzing metabolic changes in the rat barrel cortex using functional magnetic resonance spectroscopy during whisker stimulation. Baseline metabolite spectra are compared with stimulated spectra to detect lactate increase in the barrel cortex, confirming successful neuronal activation.

Source: Villarreal, S., et. al., Measuring Synaptic Vesicle Endocytosis in Cultured Hippocampal Neurons. J. Vis. Exp. (2017)This video demonstrates the analysis of synaptic vesicle endocytosis in cultured hippocampal neurons through horseradish peroxidase labeling and electron microscopy.

Source: Becker-Kojić, Z. A., et. al., GM-Free Generation of Blood-Derived Neuronal Cells. J. Vis. Exp. (2021)The video demonstrates a protocol for preparing neural cells derived from reprogrammed peripheral blood cells for fluorescence microscopy, showcasing distinct cell types and developmental stages through immunofluorescence imaging.

Source: McLeod, F., et al. Evaluation of Synapse Density in Hippocampal Rodent Brain Slices. J. Vis. Exp. (2017).This video demonstrates a method for visualizing synaptic markers in hippocampal brain slices using confocal immunofluorescence analysis. The slices are immunostained with primary antibodies targeting presynaptic and postsynaptic markers, followed by fluorophore-conjugated secondary antibodies. The labeled markers are then visualized using confocal microscopy to evaluate the synaptic...

Source: Lerchundi, R., et. al. Imaging of Intracellular ATP in Organotypic Tissue Slices of the Mouse Brain using the FRET-based Sensor ATeam1.03YEMK. J. Vis. Exp. (2019)This video demonstrates the use of FRET(Fluorescence Resonance Energy Transfer)-based sensors to measure intracellular ATP levels in organotypic mouse hippocampal slices, enabling real-time visualization of ATP dynamics in neurons and astrocytes under physiological and experimental conditions.

Source: Espinoza, R., et al. Real-Time, Two-Color Stimulated Raman Scattering Imaging of Mouse Brain for Tissue Diagnosis. J. Vis. Exp. (2022). The video demonstrates two-color stimulated Raman scattering (SRS) imaging of mouse brain tissue sections. Two synchronized laser beams are directed onto the tissue section to excite molecular vibrations, resulting in a relative intensity change in the beams. Lipids and proteins in the tissue are detected using distinct frequency pairs of the laser...

Source: Olesen, M. V., et al. The Optical Fractionator Technique to Estimate Cell Numbers in a Rat Model of Electroconvulsive Therapy. J. Vis. Exp. (2017). The video demonstrates the technique for quantifying newly generated neurons in brain tissue. Hippocampal tissue slices containing Bromodeoxyuridine (BrdU)-labeled neurons were stained using immunohistochemistry and subsequently quantified across the tissue thickness using the optical fractionator technique.

Source: Guan, W., et. al. Visualize Drosophila Leg Motor Neuron Axons Through the Adult Cuticle. J. Vis. Exp. (2018) This video demonstrates imaging of Drosophila legs with green fluorescent protein-expressing motor neurons using confocal microscopy. A laser and two detectors capture GFP and cuticle autofluorescence. Images are processed by splitting channels, subtracting autofluorescence, and merging into a colored composite image to visualize axons within the leg segment.

Source: Lauer, S. M., et al. Visualization of Cortical Modules in Flattened Mammalian Cortices. J. Vis. Exp. (2018) This video demonstrates a method to visualize the cortical modules in flattened brain sections using histochemical staining. Pre-fixed sections are treated with a straining reagent that highlights active neural clusters, forming dark, high-contrast regions. After mounting and dehydration, cortical modules appear under a bright-field microscope as dark, patchy patterns.

Source: Hidmark, A. S., et al. Analysis of Immune Cells in Single Sciatic Nerves and Dorsal Root Ganglion from a Single Mouse Using Flow Cytometry. J. Vis. Exp. (2017). This video demonstrates the use of flow cytometry to analyze immune cells in mouse sciatic nerves and dorsal root ganglia (DRGs). The process involves labeling immune cells with fluorophore- and biotin-tagged antibodies, stabilizing and permeabilizing the cells, and using fluorescent markers to detect cell-surface and nuclear...

Source: Morsch, M., et. al., Triggering Cell Stress and Death Using Conventional UV Laser Confocal Microscopy. J. Vis. Exp. (2017) In this video, we explore the technique of high-intensity UV laser ablation for precisely targeting and studying individual neurons in transgenic zebrafish. We demonstrate how to prepare, immobilize, and visualize neuronal responses, highlighting the cellular dynamics of injury and recovery.

Source: Lunelli, L., et. al. Peering at Brain Polysomes with Atomic Force Microscopy. J. Vis. Exp.(2016).This video demonstrates the imaging of polysomes using atomic force microscopy. A nickel-ions-coated mica sheet anchors RNA with attached ribosomes. The sample is washed, dried, and mounted onto the microscope stage. The cantilever tip scans the sample surface, recording laser deflections to map the topology. Software is used to correct distortions and visualize high-resolution polysome...

Source: Kimmelmann-Shultz, B., et. al. Using Near-infrared Fluorescence and High-resolution Scanning to Measure Protein Expression in the Rodent Brain. J. Vis. Exp. (2019) This video demonstrates a near-infrared fluorescence and high-resolution scanning method for measuring protein expression in the rodent brain.

Source: Hamid, H. S., et al. Three-dimensional Imaging and Analysis of Mitochondria within Human Intraepidermal Nerve Fibers. J. Vis. Exp. (2017) This video demonstrates the method for visualizing nerve-specific mitochondria using three-dimensional imaging. It outlines the process of acquiring sequential scans of pre-labeled intraepidermal nerve fibers and generating 3D surface images to isolate and display mitochondria in relation to nerve structures.

Source: Mukherjee, K., et. al. Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy. J. Vis. Exp. (2016)This video demonstrates the preparation, imaging, and analysis of mouse brain tissue using a serial block-face scanning electron microscope (SBFSEM) to visualize mitochondrial ultrastructure, enabling precise mapping of their morphology and spatial distribution in axonal and dendritic neuronal compartments.

Source: Laboissonniere, et. al. Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells. J. Vis. Exp. (2017). This video demonstrates a fluorescent tracing technique to identify retinal ganglion cell (RGC) subtypes in a transgenic mouse retina. The process involves securing the isolated retina in a recording chamber, maintaining cell viability with oxygenated perfusion, and targeting fluorescently labeled RGCs using a pipette with a tracer. By analyzing dendritic morphology and...

Take a fixed section of mouse cortical brain tissue exhibiting neuronal axons and dendrites. The dendrites possess protrusions, known as dendritic spines, which form synapses with axons.Incubate the tissue with osmium-ferrocyanide, which binds to lipids, followed by another osmium application, which enhances structural contrast for imaging.Stain with a heavy metal compound that binds to macromolecules and enhances contrast.Dehydrate using increasing alcohol concentrations for resin...

Source: Mizuno, H., et al. In Vivo Two-photon Imaging of Cortical Neurons in Neonatal Mice. J. Vis. Exp. (2018)This video showcases two-photon microscopy being used to image neurons in the brain of an anesthetized transgenic mouse pup. The two-photon laser allows for deeper imaging with high spatial resolution and minimal light scattering, enabling the detailed capture of neuronal morphology, including dendritic projections.

Source: Lark, A. R., et. al., In Vivo Functional Brain Imaging Approach Based on Bioluminescent Calcium Indicator GFP-aequorin. J. Vis. Exp. (2016)This video demonstrates real-time imaging of calcium dynamics using Green fluorescent protein-aequorin bioluminescence in Drosophila's deep brain structures.

Source: Muto, A., et al. Ablation of a Neuronal Population Using a Two-photon Laser and Its Assessment Using Calcium Imaging and Behavioral Recording in Zebrafish Larvae. J. Vis. Exp. (2018) In this video, a two-photon laser ablation procedure is demonstrated, enabling the selective destruction of fluorescent neurons in agarose-immobilized zebrafish larvae. High-resolution imaging before and after the procedure confirms efficient neuronal damage, as observed by the absence of fluorescence.

Source: Winkle, C. C., et al. Utilizing Combined Methodologies to Define the Role of Plasma Membrane Delivery During Axon Branching and Neuronal Morphogenesis. J. Vis. Exp. (2016)This video demonstrates a live-imaging technique using differential interference contrast (DIC) microscopy to observe real-time axonal branching in cortical neurons. Time-lapse videos capture the effects of netrin-1 treatment, a signaling molecule that induces localized exocytosis and cytoskeletal rearrangements in...

Source: Zhilyakov, N. V. et. al., Registration of Calcium Transients in Mouse Neuromuscular Junction with High Temporal Resolution using Confocal Microscopy. J. Vis. Exp. (2021)This video demonstrates the imaging technique of recording fast calcium transients at nerve endings using confocal microscopy. By stimulating the nerve and capturing fluorescence changes from calcium-binding dyes, it visualizes dynamic calcium influx and clearance at the nerve ending, offering precise insights into...

Source: Ting, C., et al., Analyzing Dendritic Morphology in Columns and Layers. J. Vis. Exp. (2017)This video demonstrates the procedure of preparing a Drosophila brain, capturing horizontal and frontal image stacks of GFP-labeled medulla dendrites under a confocal microscope, and creating a 3D reconstruction to analyze their morphology across layers and columns.

Source: Lacin, E., et al. Construction of Cell-based Neurotransmitter Fluorescent Engineered Reporters (CNiFERs) for Optical Detection of Neurotransmitters In Vivo. J. Vis. Exp. (2016)This video demonstrates a technique for imaging neurotransmitter release in vivo using cell-based neurotransmitter fluorescent engineered reporters (CNiFERs), specialized reporter cells pre-injected into the mouse cortex. Positioned under a two-photon microscope, the mouse allows visualization of...

Source: Doser, R., et al. Subcellular Imaging of Neuronal Calcium Handling In Vivo. J. Vis. Exp. (2023)This video demonstrates in vivo imaging of subcellular calcium flux in the ventral nerve cord neurons of transgenic Caenorhabditis elegans strains. Two distinct calcium indicators are employed: a cytoplasmic indicator in one strain and a mitochondrial indicator in another. Neurons are observed under a fluorescence microscope to monitor real-time changes in fluorescence intensity within the...

Source: Gouder, et. al. Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells. J. Vis. Exp. (2015).This video demonstrates the imaging and analysis of dendritic spines in transduced, immunolabeled pyramidal neurons using confocal microscopy. Background noise is reduced, and dendrites are traced by estimating their diameter and length. Automated spine segmentation involves setting parameters for dendrite and spine dimensions...

Source: Creighton, B. A., et al. Visualizing and Analyzing Intracellular Transport of Organelles and Other Cargos in Astrocytes. J. Vis. Exp. (2019)This video demonstrates the visualization of intracellular cargo transport in cultured astrocytes using a fluorescent acidotropic probe that selectively labels acidic endolysosomal vesicles. Time-lapse imaging and Z-stack acquisition with a confocal microscope allow tracking of fluorescently labeled cargo throughout the three-dimensional cell volume.

Source: Katsalifis, A., et al. Live Imaging of the Mitochondrial Glutathione Redox State in Primary Neurons using a Ratiometric Indicator. J. Vis. Exp. (2021)This video demonstrates the imaging of mitochondrial redox state in primary neurons using a ratiometric fluorescent indicator. By applying two excitation wavelengths under a fluorescence microscope, the fluorescence intensity ratio is measured to assess mitochondrial oxidation. The protocol includes N-methyl-D-aspartate (NMDA) stimulation...

Source: Bagheri, M., et. al. Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes. J. Vis. Exp. (2015).This video demonstrates the imaging of fluorescently labeled astrocytes in a mouse brain section using a confocal microscope. The brain section is positioned under the appropriate objective lens, and suitable fluorophores and filters are selected. After optimizing the exposure automatically, the scanning parameters are defined to ensure high-resolution 2D images. Z-stack...

Source: Weber, R. Z., et al., Intracerebral Transplantation and In Vivo Bioluminescence Tracking of Human Neural Progenitor Cells in the Mouse Brain. J. Vis. Exp. (2022)This video demonstrates the method for in vivo bioluminescence imaging of genetically modified human neural progenitor cells injected in a mouse brain. The process involves luciferin injection, imaging preparation, and detection of bioluminescent signals from the transplanted cells at the injection site.

Source: Bannai, H., et. al., Dissection of Local Ca2+ Signals in Cultured Cells by Membrane-targeted Ca2+ Indicators. J. Vis. Exp. (2019)The video demonstrates fluorescence imaging to observe compartment-specific spontaneous calcium dynamics in astrocytes by sequentially monitoring calcium-sensitive proteins localized on the plasma membrane and endoplasmic reticulum.

Source: Marinello, M., et al. Characterization of Neuromuscular Junctions in Mice by Combined Confocal and Super-Resolution Microscopy. J. Vis. Exp. (2021)This video demonstrates the preparation, immunostaining, and imaging of neuromuscular junctions in rat muscle tissue using confocal and super-resolution microscopy to visualize and analyze presynaptic and postsynaptic structures.

Source: Chiu, S., et al. Phase Contrast Magnetic Resonance Imaging in the Rat Common Carotid Artery. J. Vis. Exp. (2018).This video demonstrates phase contrast magnetic resonance imaging (PC-MRI) to measure blood flow in the common carotid artery of a rat. After securing an anesthetized rat on the MRI bed and ensuring stable physiological parameters, the common carotid artery is scanned to capture images at defined intervals. Blood flow is then computed from these images to evaluate changes...

Source: Hage, B. D. et. al., Functional Transcranial Doppler Ultrasound for Monitoring Cerebral Blood Flow. J. Vis. Exp. (2021) This video demonstrates the use of Doppler ultrasound as a functional imaging tool to measure cerebral blood flow velocity, or CBFV in real time. It highlights how frequency shifts in the middle cerebral artery during tasks like breath-holding reveal changes in CBFV, offering insights into brain activity and vascular dynamics.

Position the patient's head inside the radiofrequency, or RF, coil of a magnetic resonance imaging, or MRI, machine.Initiate the time-of-flight magnetic resonance angiography or TOF MRA, a non-invasive technique for visualizing blood vessels.Select a tissue slice for imaging to visualize arteries and veins.Apply an RF pulse to excite the protons within the selected imaging slice. These protons release energy, which is detected as an MR signal.Repeated application of RF pulses saturates the MR...

Perivascular spaces (PVS) are fluid-filled spaces around the brain blood vessels involved in fluid drainage.To examine alterations in PVS during a small vessel stroke, perform magnetic resonance imaging (MRI) of the basal ganglia region in the patient’s brain.The imaging protocol includes the T2-weighted fast spin echo and fluid-attenuated inversion recovery (FLAIR) sequences.T2-weighted imaging enhances the contrast between cerebrospinal fluid (CSF)-filled PVS and surrounding tissue.FLAIR...

Source: Nishimura, C. et al. Quantification of Cerebral Vascular Architecture using Two-photon Microscopy in a Mouse Model of HIV-induced Neuroinflammation. J. Vis. Exp. (2016). This video demonstrates the in vivo visualization of cortical capillaries in the mouse brain using two-photon microscopy. It outlines the steps for injecting a fluorescent dye into an anesthetized mouse with a thin-skull cortical window, preparing the setup for imaging, and acquiring detailed images of brain...

Position a human patient with internal carotid stenosis, a condition characterized by narrowing of the internal carotid artery, on the imaging table for digital subtraction angiography (DSA). Insert an angiocatheter into the common carotid artery at the fourth cervical vertebra level. Capture a pre-contrast X-ray image to record background structures like bones and soft tissues using X-ray irradiation. Administer an iodine-based contrast medium into the carotid artery.  The contrast medium...

Start with a human patient with cerebral vasculitis, which causes inflammation and increased permeability of blood vessels in the brain.Place the patient's head inside the radiofrequency, or RF, coil of a magnetic resonance imaging, or MRI, machine.Initiate magnetic resonance angiography, or MRA, which uses RF pulses to image blood flow.Protons in flowing blood generate strong signals, making blood vessels appear bright, while weak signals from stationary tissues result in a dark...

Source: Tan, Z., et al., Construction and Application of Cerebral Functional Region-Based Cerebral Blood Flow Atlas Using Magnetic Resonance Imaging-Arterial Spin Labeling. J. Vis. Exp. (2024).This video demonstrates the method to construct a cerebral blood flow atlas by integrating magnetic resonance imaging or MRI-arterial spin labeling data with segmented brain regions, visualizing blood flow patterns, and quantifying flow levels across functional areas.

Source: Kim, D., et. al. Combined Near-infrared Fluorescent Imaging and Micro-computed Tomography for Directly Visualizing Cerebral Thromboemboli. J. Vis. Exp. (2016)This video demonstrates visualization of cerebral thrombus in mice using micro-computed tomography (micro-CT) imaging. A cerebral thrombus mouse model is injected with fibrin-targeted gold nanoparticles acting as a contrasting agent. The mouse is placed on the bed of a micro-CT machine, and images are acquired from multiple angles.

Source: Giustetto, P., et. al., Non-invasive Parenchymal, Vascular and Metabolic High-frequency Ultrasound and Photoacoustic Rat Deep Brain Imaging. J. Vis. Exp. (2015)In this video, we demonstrate the use of high-frequency ultrasound and photoacoustic imaging to study the vasculature and hemoglobin content in the rat brain. This method provides detailed insights into cerebral perfusion and blood oxygenation, enabling non-invasive analysis of brain vascular structures and oxygen distribution.

Source: Kalva, S. K., et al., Pulsed Laser Diode-Based Desktop Photoacoustic Tomography for Monitoring Wash-In and Wash-Out of Dye in Rat Cortical Vasculature. J. Vis. Exp. (2019)This video demonstrates the procedure for using photoacoustic imaging to observe changes in the cortical vessels of an anesthetized rat. The process includes baseline imaging, dye injection, and analysis of dye absorption and clearance during wash-in and wash-out.

Source: Menezes Forti, R. et al. Real-Time Monitoring of Neurocritical Patients with Diffuse Optical Spectroscopies. J. Vis. Exp. (2020)This video demonstrates the use of Diffuse Correlation Spectroscopy (DCS) to measure cerebral blood flow in humans. It outlines the steps for preparing the system, calibrating the probe, positioning it on the participant’s forehead, acquiring scattered light data, and analyzing intensity fluctuations to interpret blood flow dynamics in the brain.

Source: Kim, D. E., et al. Combined Near-infrared Fluorescent Imaging and Micro-computed Tomography for Directly Visualizing Cerebral Thromboemboli. J. Vis. Exp. (2016)This video demonstrates near-infrared fluorescent (NIRF) imaging to visualize thrombi in excised brain tissue labeled with a fibrin-specific probe. Near-infrared light excites the probe, causing the thrombus to fluoresce, enabling high-contrast thrombi visualization in the major cerebral artery and small cortical blood vessels.

Source: Villaseñor, R and Collin. L. High-resolution Confocal Imaging of the Blood-brain Barrier: Imaging, 3D Reconstruction, and Quantification of Transcytosis. J. Vis. Exp. (2017)This video demonstrates high-resolution 3D imaging of the blood-brain barrier (BBB) using confocal microscopy, showing antibody-stained mouse brain sections to analyze BBB components and intracellular structures, applicable for studying brain homeostasis, neurovascular interactions, and disease-related BBB...

Source: Sweeney, A. M., et al. In Vivo Imaging of Cerebrospinal Fluid Transport through the Intact Mouse Skull using Fluorescence Macroscopy. J. Vis. Exp. (2019)This video demonstrates the process of visualizing cerebrospinal fluid (CSF) flow in a mouse brain using fluorescence imaging. A fluorescent tracer is injected into the cisterna magna (CM), allowing its movement with CSF to be tracked through the subarachnoid and perivascular spaces. Time-lapse imaging captures the tracer's journey,...

Source: Breid, S., et. al. Bioluminescence Imaging of Neuroinflammation in Transgenic Mice After Peripheral Inoculation of Alpha-Synuclein Fibrils. J. Vis. Exp. (2017)This video demonstrates the bioluminescence imaging of neuroinflammation in transgenic mice, showcasing luciferase-luciferin reactions in activated astrocytes. The protocol enables non-invasive quantification of astrocytic activation, aiding studies on CNS inflammation and therapeutic efficacy.

Source: Nyström, S., et al., Imaging Amyloid Tissues Stained with Luminescent Conjugated Oligothiophenes by Hyperspectral Confocal Microscopy and Fluorescence Lifetime Imaging. J. Vis. Exp. (2017).This video demonstrates analyzing amyloid structures with fluorescence lifetime imaging microscopy or FLIM, using hFTAA dye to reveal compact cores as blue/green and unstable peripheries as red/yellow in color-coded images, reflecting amyloid organization.

Source: Bosco, A., et al. In Vivo Dynamics of Retinal Microglial Activation During Neurodegeneration: Confocal Ophthalmoscopic Imaging and Cell Morphometry in Mouse Glaucoma. J. Vis. Exp. (2015) This video demonstrates in vivo imaging of retinal microglia in a mouse model of glaucoma. A transgenic mouse with fluorescent protein-expressing retinal microglia is positioned under an ophthalmoscope. Infrared illumination is used to locate the optic nerve head (ONH), and the focal plane is...

Source: Maiti, P. et. al.,. Labeling and Imaging of Amyloid Plaques in Brain Tissue Using the Natural Polyphenol Curcumin. J. Vis. Exp. (2019)This video demonstrates the imaging procedure of amyloid-beta plaques in brain tissue sections using immunolabeling and curcumin staining. Immunolabeling provides specificity for amyloid-beta, while curcumin selectively binds β-sheet-rich fibrils, enhancing visualization. The co-localization of red and green fluorescence confirms the presence of plaques.

Position the head of a patient with multiple sclerosis inside the radiofrequency or RF coil of an MRI machine.Begin fluid-attenuated inversion recovery or FLAIR imaging. Select a brain slice containing lesions near CSF-rich areas.The system generates a strong magnetic field, aligning protons in healthy and lesioned brain tissue and CSF along its direction, creating net magnetization.Apply an inversion RF pulse to flip the magnetization of all protons, aligning them opposite to the magnetic...

Source: Zaeck, L., et al. High-Resolution 3D Imaging of Rabies Virus Infection in Solvent-Cleared Brain Tissue. J. Vis. Exp. (2019). This video demonstrates the process of preparing and imaging mouse brain tissue infected with the rabies virus (RABV) to evaluate infection progression. It outlines key steps, including tissue staining with fluorescent markers, dehydration, clearing, and mounting for confocal laser scanning microscopy, culminating in the generation of a three-dimensional...

Source: Bisht, K., et. al. Correlative Light and Electron Microscopy to Study Microglial Interactions with β-Amyloid Plaques. J. Vis. Exp. (2016) This video demonstrates the visualization and mapping of Methoxy-X04-labeled amyloid plaques in Alzheimer’s disease mouse brain sections using fluorescence and bright-field microscopy, enabling precise correlation of plaques with anatomical structures for studying Alzheimer’s pathology.

Source: Ouyang, Y., et al. Simultaneous PET/MRI Imaging During Mouse Cerebral Hypoxia-ischemia. J. Vis. Exp. (2015)This video demonstrates a technique to assess cerebral hypoxia injury via simultaneous positron-emission tomography (PET) and magnetic resonance imaging (MRI). An anesthetized mouse undergoes common carotid artery (CCA) ligation, reducing blood flow to one brain hemisphere and predisposing it to hypoxia-induced injury. PET and MRI imaging evaluate glucose metabolism and structural...

Source: Krishnamurthy, K. et al. Real-Time Fluorescent Measurement of Synaptic Functions in Models of Amyotrophic Lateral Sclerosis. J. Vis. Exp. (2021)This video demonstrates real-time calcium imaging to monitor synaptic activity in ALS-mutant neurons expressing a genetically encoded calcium biosensor. It outlines the steps for preparing the neurons for imaging, stimulating calcium dynamics, and recording fluorescence to measure real-time changes in intracellular calcium levels, which reflect...

Source: Ciraku, L., et. al. An Ex Vivo Brain Slice Model to Study and Target Breast Cancer Brain Metastatic Tumor Growth. J. Vis. Exp. (2021).This video demonstrates the imaging of luciferase-expressing tumor cells in an organotypic mouse brain slice. Luciferin is added to the medium, and the plate is placed inside the chamber of the in vivo imaging system. Parameters for image capture are adjusted, and the tumor's shape and size are defined. The bioluminescent signals emitted by the tumor...

Source: Arango-Lievano, M. et. al., Longitudinal In Vivo Imaging of the Cerebrovasculature: Relevance to CNS Diseases. J. Vis. Exp. (2016)This video demonstrates in vivo two-photon imaging to visualize fluorescently labeled amyloid plaques and cerebral vasculature. Blue fluorescence marks plaques, while green fluorescence highlights the cerebral blood vessels. A 3D map of the region of interest and high-resolution mosaic imaging reveal detailed interactions of amyloid plaques with cerebral...

Source: Clark, A.J., et al. Bioluminescence Imaging of an Immunocompetent Animal Model for Glioblastoma. J. Vis. Exp. (2016)This video demonstrates bioluminescence imaging to track glioblastoma progression in an immunocompetent mouse model, using luciferase-expressing tumor cells and luciferin to quantify tumor growth non-invasively.

Source: Parker, J. J., et al. A Human Glioblastoma Organotypic Slice Culture Model for Study of Tumor Cell Migration and Patient-specific Effects of Anti-Invasive Drugs. J. Vis. Exp. (2017)This video showcases the imaging of glioblastoma tissue slices expressing green fluorescent protein (GFP) via confocal microscopy. High-resolution images are captured at consistent intervals to track tumor cell movement and direction.

Source: Lutz, D., et.al. Assessment of Ultrastructural Neuroplasticity Parameters After In Utero Transduction of the Developing Mouse Brain and Spinal Cord. J. Vis. Exp. (2019).This video demonstrates the preparation and transmission electron microscopy (TEM) analysis of a brain section from a mouse pup. The protocol starts with osmium tetroxide-fixed tissue embedded in resin, followed by precise trimming to isolate the region of interest and ultramicrotomy to produce semithin and ultrathin...

Source: Inal, M. A. et. al., Retrograde Tracing of Drosophila Embryonic Motor Neurons Using Lipophilic Fluorescent Dyes. J. Vis. Exp. (2020)This video demonstrates the method of retrograde labeling of Drosophila motor neurons using lipophilic dyes. The dye enters the axon, travels retrogradely, and labels the neurons green, allowing detailed visualization of their morphology and projections under a confocal microscope.

Source: Flatz, W. H. et al. In Vivo Morphometric Analysis of Human Cranial Nerves Using Magnetic Resonance Imaging in Menière's Disease Ears and Normal Hearing Ears. J. Vis. Exp. (2018).This video demonstrates the use of MRI to analyze cranial nerve morphology in the ears of patients suffering from a chronic inner ear disorder. It outlines the steps for performing a high magnetic field MRI scan on the patient, reconstructing the high-resolution 3D cross-sectional images of the cranial nerves,...

Source: Braeckman, K., et. al. Advanced Diffusion Imaging in The Hippocampus of Rats with Mild Traumatic Brain Injury. J. Vis. Exp. (2019)This video demonstrates the use of diffusion-weighted imaging to assess microstructural changes in a rat hippocampus following mild traumatic brain injury (mTBI), highlighting axonal injury through precise MRI scanning and diffusion analysis.

Source: Papadelis, C., et al., Interictal High Frequency Oscillations Detected with Simultaneous Magnetoencephalography and Electroencephalography as Biomarker of Pediatric Epilepsy. J. Vis. Exp. (2016). This video demonstrates the method of using electroencephalography (EEG) and magnetoencephalography (MEG) recordings to identify interictal epileptiform discharges (IEDs) and high-frequency oscillations (HFOs) to locate seizure-prone regions in the brain.

Source: Huang, Y. et. al., Longitudinal Morphological and Physiological Monitoring of Three-dimensional Tumor Spheroids Using Optical Coherence Tomography. J. Vis. Exp. (2019)This video demonstrates the use of optical coherence tomography (OCT) to monitor tumor spheroids in a multi-well plate by capturing high-resolution cross-sectional images. By analyzing light reflections from cellular structures, OCT constructs 3D models to assess morphological features like size and shape while also...

Source: Lahne, M., et.al. Culture of Adult Transgenic Zebrafish Retinal Explants for Live-cell Imaging by Multiphoton Microscopy. J. Vis. Exp. (2017)This video demonstrates live-cell imaging of Muller glial nuclear migration in agarose-embedded zebrafish retinal explants following light-induced photoreceptor damage. Tumor necrosis factor-alpha (TNF-α) released by damaged photoreceptors activates Muller glial cells, triggering nuclear migration through the inner and outer nuclear layers for...

Source: Bénard, M., et al. Ex Vivo Imaging of Postnatal Cerebellar Granule Cell Migration Using Confocal Macroscopy. J. Vis. Exp. (2015)This video demonstrates a confocal macroscopic method to track the ex vivo migration of granule cells in cerebellar slices from postnatal rat brains.

Source: Daynac, M., et. al. Cell Sorting of Neural Stem and Progenitor Cells from the Adult Mouse Subventricular Zone and Live-imaging of their Cell Cycle Dynamics. J. Vis. Exp. (2015)This video demonstrates time-lapse imaging of neural stem cells (NSCs) from a transgenic mouse brain using a confocal laser scanning microscope. NSCs fluoresce red during the G1 phase and are non-fluorescent in other cell-cycle phases. An adhered NSC culture is placed in the imaging chamber, imaging parameters are...

Source: Williams, A. L., et al. Multi-Photon Time Lapse Imaging to Visualize Development in Real-time: Visualization of Migrating Neural Crest Cells in Zebrafish Embryos. J. Vis. Exp. (2017)This video showcases a multi-photon time-lapse imaging protocol to visualize the migration of neural crest cells in a zebrafish embryo in real-time with high resolution.

Source: Jeong, S. Visualization of the Axonal Projection Pattern of Embryonic Motor Neurons in Drosophila. J. Vis. Exp. (2017)This video demonstrates the visualization of axonal projections in Drosophila embryos. Immunolabeling of motor neurons, precise dissection to expose neuronal structures, and differential interference contrast microscopy collectively reveal detailed neuronal architecture, emphasizing the axonal projection patterns.

Source: Canovic, E. P., et. al., Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry. J. Vis. Exp. (2016)The video demonstrates using impact indentation to measure the mechanical properties of a hydrated mouse brain tissue, including stiffness, energy dissipation, and damping, through probe displacement and velocity analysis.

Source: Portela-Lomba, M., et. al. Coculture of Axotomized Rat Retinal Ganglion Neurons with Olfactory Ensheathing Glia, as an In Vitro Model of Adult Axonal Regeneration. J. Vis. Exp. (2020).This video demonstrates imaging and quantification of axonal regeneration in axotomized rat retinal ganglion neurons (RGNs) co-cultured with immortalized human olfactory ensheathing glia cells. RGNs are immunolabeled, with red somas and green axons. Images were captured using an epifluorescence microscope,...

Source: Changou, C. A., et. al. Live Images of GLUT4 Protein Trafficking in Mouse Primary Hypothalamic Neurons Using Deconvolution Microscopy. J. Vis. Exp. (2017).This video showcases the imaging of insulin-induced GLUT4 translocation in hypothalamic neurons, employing deconvolution microscopy to capture and analyze GFP-GLUT4 trafficking dynamics with high resolution.

Source: Kennedy, L. H., et. al. Visualization and Live Imaging of Oligodendrocyte Organelles in Organotypic Brain Slices Using Adeno-associated Virus and Confocal Microscopy. J. Vis. Exp. (2017)This video demonstrates the imaging of oligodendrocyte mitochondria in organotypic mouse brain slices. The slice is placed inside a bath chamber with continuous fluid circulation and controlled temperature. After setting up various parameters of the confocal microscope, time-lapse images of mitochondria...

Source: Etienne, F. et al. Two-photon Imaging of Microglial Processes' Attraction Toward ATP or Serotonin in Acute Brain Slices. J. Vis. Exp. (2019)This video demonstrates the use of two-photon microscopy to study the attraction of microglial processes toward an injected compound in brain slices. It provides an overview of preparing mouse brain slices, injecting a chemoattractant test compound, and imaging fluorescently labeled microglia to visualize their responses.

Source: Wang, Z., et al. Transpupillary Two-Photon In Vivo Imaging of the Mouse Retina. J. Vis. Exp. (2021).This video demonstrates a technique for in vivo retinal imaging using two-photon microscopy. Anesthetized mice are prepared for imaging by securing their heads, Applying eye lubricant, and placing a coverslip over the eye. Retinal ganglion cells (RGCs) expressing fluorescent proteins are first visualized using epifluorescence for alignment. Finally, two-photon imaging is employed,...

Source: Bisht, K., et al. Precise brain mapping to perform repetitive in vivo imaging of neuro-immune dynamics in mice. J. Vis. Exp. (2020)This video demonstrates fluorescence imaging of neuro-immune dynamics in a transgenic mouse with a skull implant. Vascular and neuronal stability is imaged alongside dynamic microglial changes, reflecting immune responses to neuronal activity.

Source: Shannonhouse, J., et al.In Vivo Calcium Imaging of Neuronal Ensembles in Networks of Primary Sensory Neurons in Intact Dorsal Root Ganglia. J. Vis. Exp. (2023).The video demonstrates an in vivo calcium imaging technique to monitor neuronal activity in the dorsal root ganglia (DRG) of a transgenic mouse. DRG neurons express a calcium indicator that increases fluorescence intensity upon binding to calcium. Mechanical or thermal stimuli applied to a hind paw generate action potentials that...

Source: Hellerman, M. B., et al. Live-imaging of the Drosophila Pupal Eye. J. Vis. Exp. (2015)The video demonstrates a live-imaging technique to study eye patterning in a Drosophila melanogaster pupa. Green fluorescent protein (GFP)-tagged markers enable visualization of cellular organization and differentiation during the formation of the developing eye structure.

Source: Ulivi, A. F., et. al. Longitudinal Two-Photon Imaging of Dorsal Hippocampal CA1 in Live Mice. J. Vis. Exp. (2019) This video demonstrates longitudinal two-photon imaging of fluorescently-labeled pyramidal neurons in a live mouse, showcasing the preparation, cannula alignment, and imaging of dendrites and dendritic spines to study neuronal structure in the hippocampal CA1 region.

Source: Gómez-Villafuertes, R., et. al., Live Imaging Followed by Single Cell Tracking to Monitor Cell Biology and the Lineage Progression of Multiple Neural Populations. J. Vis. Exp. (2017) The video demonstrates the process of preparing, imaging, and tracking adult neural stem cells in real time to study cellular behaviors, including division and differentiation.

Source: Volpe, B. A., et al. Confocal Microscope-Based Laser Ablation and Regeneration Assay in Zebrafish Interneuromast Cells. J. Vis. Exp. (2020) This video demonstrates monitoring interneuromast cell recovery in zebrafish using confocal microscopy, tracking cell death and repair through time-lapse fluorescence imaging.

Source: Fried, D. E., Gulbransen, B. D. In Situ Ca2+ Imaging of the Enteric Nervous System. J. Vis. Exp. (2015)This video demonstrates calcium imaging to visualize and analyze the activity of enteric neurons and glia in mouse Colonic Myenteric plexus preparations.

Source: Jagodzinska, J., et. al., Optical Coherence Tomography: Imaging Mouse Retinal Ganglion Cells In Vivo. J. Vis. Exp. (2017) In this video, we demonstrate the use of spectral-domain optical coherence tomography (SD-OCT) to image retinal layers and assess structural changes in a genetically modified mouse model with optic neuropathy.

Source: Chaney, A. M., et.al. PET Imaging of Neuroinflammation Using [11C]DPA-713 in a Mouse Model of Ischemic Stroke. J. Vis. Exp. (2018). This video demonstrates a technique for in vivo imaging of neuroinflammation in a mouse model of ischemic stroke using a TSPO-specific radiotracer. Following injection, the radiotracer binds to TSPO, a protein located on the outer mitochondrial membrane and overexpressed in activated immune cells. A PET/CT scanner detects the radiotracer's distribution and...

Source: Choi, J. P. et al. Induction and Micro-CT Imaging of Cerebral Cavernous Malformations in Mouse Model. J. Vis. Exp. (2017)This video demonstrates the use of micro-CT imaging to visualize cerebral cavernous malformation (CCM) lesions in a mouse brain. It details the steps for sample preparation, imaging, and 3D image reconstruction to evaluate the density and location of CCM lesions in brain tissue.

Source: Schmitz, K., et al., Bioluminescence and Near-infrared Imaging of Optic Neuritis and Brain Inflammation in the EAE Model of Multiple Sclerosis in Mice. J. Vis. Exp. (2017).This video demonstrates the method for visualizing and monitoring Experimental Autoimmune Encephalomyelitis or EAE-induced inflammation in the optic nerve using bioluminescence imaging. It includes positioning the mouse, reagent injection, and capturing sequential images to monitor changes in bioluminescence over time.

Source: Ishimoto, H. et. al., Ex Vivo Calcium Imaging for Visualizing Brain Responses to Endocrine Signaling in Drosophila. J. Vis. Exp. (2018) This video demonstrates calcium imaging to study Drosophila brain responses to neuropeptides. Neurons expressing a fluorescent calcium indicator reveal intracellular calcium dynamics and functional responses to signaling molecules.

Source: Al Omran, A. J., et al. Live Imaging of the Ependymal Cilia in the Lateral Ventricles of the Mouse Brain. J. Vis. Exp. (2015). This video demonstrates a live-imaging technique using differential interference contrast (DIC) microscopy to observe the beating of ependymal cilia in sagittal mouse brain sections. Ependymal cilia propel cerebrospinal fluid (CSF), and their activity is recorded in brain sections maintained in a nutrient-rich medium and imaged in a climate-controlled chamber.

Source: Pigazzini, M. L., et. al. Characterization of Amyloid Structures in Aging C. Elegans Using Fluorescence Lifetime Imaging. J. Vis. Exp. (2020).This video demonstrates the use of fluorescence lifetime imaging microscopy (FLIM) to assess polyQ protein aggregation in C. elegans neurons, comparing control and chaperone protein-deficient worms. Increased aggregation in chaperone-deficient worms promotes energy transfer between clustered fluorophores, reducing fluorescence lifetime.

Source: Landeira, B. S.,et al., Live Imaging of Primary Cerebral Cortex Cells Using a 2D Culture System. J. Vis. Exp. (2017)The video demonstrates the use of time-lapse imaging to track fluorescently labeled cortical progenitors, monitor their division and differentiation, and study lineage development in primary cerebral cortex...

Source: Lee, H. et. al., Successful In vivo Calcium Imaging with a Head-Mount Miniaturized Microscope in the Amygdala of Freely Behaving Mouse. J. Vis. Exp. (2020)This video demonstrates in vivo calcium imaging in a mouse using a gradient refractive index, or GRIN lens, and a miniaturized microscope. The setup combines head fixation within a frictionless mobile cage system, stimulating neurons and triggering calcium ion influx. The GRIN lens captures calcium signaling in the brain, enabling...

Source: Thapa, R., et. al., Stereotaxic Viral Injection and Gradient-Index Lens Implantation for Deep Brain In Vivo Calcium Imaging. J. Vis. Exp. (2021)The video demonstrates real-time calcium imaging using a miniscope in a transduced mouse, correlating neuronal activity with behavior.

Source: Moore, J. D., et al. Juxtacellular Monitoring and Localization of Single Neurons within Sub-cortical Brain Structures of Alert, Head-restrained Rats. J. Vis. Exp. (2015)This video demonstrates the method of juxtacellular recording and staining in a restrained, awake rat. The procedure involves recording signals from neurons and injecting dye to precisely localize the recording site. This technique allows accurate mapping of neural activity to the brain's anatomical structure.

Source: Schramm, P. et al. In vivo Imaging of Fully Active Brain Tissue in Awake Zebrafish Larvae and Juveniles by Skull and Skin Removal. J. Vis. Exp. (2021)This video demonstrates the in vivo imaging of cerebellar neurons in transgenic zebrafish larvae, which express fluorescent proteins in Purkinje neurons. The process involves anesthetizing the larvae, immobilizing them in agarose, and carefully removing the pigmented skin to enhance light penetration and fluorescence intensity. Finally,...

Source: Ing-Esteves, S. & Lefebvre, J. L. Time-Lapse Imaging of Neuronal Arborization using Sparse Adeno-Associated Virus Labeling of Genetically Targeted Retinal Cell Populations. J. Vis. Exp. (2021)This video demonstrates the use of confocal microscopy to visualize dendritic dynamics in live mouse retinal explants. It outlines the steps for stabilizing the retina under a confocal microscope, performing epifluorescence imaging to visualize starburst amacrine interneurons, and capturing...

Source: Kamei, R., et. al., In Vivo Chronic Two-Photon Imaging of Microglia in the Mouse Hippocampus. J. Vis. Exp. (2022)The video demonstrates the setup and imaging process for in vivo two-photon microscopy of microglial dynamics in the hippocampal CA1 (Cornu ammonis 1) and dentate gyrus, ensuring optimal optical alignment and structural integrity assessment.

Source: Lukasz, D., et al. In Vivo Calcium Imaging of Lateral-line Hair Cells in Larval Zebrafish. J. Vis. Exp. (2018)This video demonstrates live imaging of calcium influx in the lateral-line hair cells of a paralyzed transgenic zebrafish larva using a confocal microscope. Mechanical stimulation of hair bundles via fluid pulses induces calcium entry through mechanotransduction channels and voltage-gated channels, which is visualized in real-time using fluorescence indicators. The method...

Source: Louth, E. L., et al. Imaging neurons within thick brain sections using the Golgi-Cox method. J. Vis. Exp. (2017)This video demonstrates imaging neurons in a Golgi-Cox stained thick brain section by setting upper and lower focus boundaries and capturing overlapping images. Multiple locations are imaged to ensure detailed neuronal projections, which are combined to create a 3D representation.

Source: Heredia, D. J., et. al. Ex Vivo Imaging of Cell-specific Calcium Signaling at the Tripartite Synapse of the Mouse Diaphragm. J. Vis. Exp. (2018) This video demonstrates fluorescence imaging of calcium dynamics at neuromuscular junctions (NMJs) in a transgenic mouse expressing genetically encoded calcium indicators. A NJM is identified by fluorescently tagged acetylcholine receptors in the diaphragm with the phrenic nerve. An image splitter is used to visualize multiple signals...

Source: Pekarek, B. T., et. al., Imaging and Quantification of Intact Neuronal Dendrites via CLARITY Tissue Clearing. J. Vis. Exp. (2021)In this video, we demonstrate the preparation, imaging, and analysis of a cleared mouse brain to examine dendritic arbors, spine morphology, and neuronal distribution using confocal microscopy and 3D reconstruction techniques.

Source: Refaeli, R., et al., Investigation of Spatial Interaction Between Astrocytes and Neurons in Cleared Brains. J. Vis. Exp. (2022) The video demonstrates the preparation of a chamber and the neuroimaging of cleared mouse hippocampal tissue using two-photon microscopy to visualize the spatial interactions between fluorescently labeled astrocytes and excitatory neurons.

Source: Chan, U., et al., Utilizing In Vivo Postnatal Electroporation to Study Cerebellar Granule Neuron Morphology and Synapse Development. J. Vis. Exp. (2021).This video demonstrates the analysis of cerebellar granule neuron development by imaging pre-fixed brain tissue slices from mice labeled with a fluorescent protein, capturing high-resolution z-stack images with a confocal microscope, and measuring structural parameters including neurite length, dendritic claw formation, surface area,...

Source: Maruoka, H., et. al. Simultaneous Imaging of Microglial Dynamics and Neuronal Activity in Awake Mice. J. Vis. Exp. (2022) This video shows a two-photon microscopy procedure for imaging neuronal activity and microglial dynamics in an awake mouse during visual stimulation, highlighting calcium transients and cellular interactions.

Source: Moye, S. L., et.al. Visualizing Astrocyte Morphology Using Lucifer Yellow Iontophoresis. J. Vis. Exp. (2019). This video demonstrates the use of fluorescent dye iontophoresis to study astrocyte morphology in fixed brain slices. It details the piercing of the astrocyte soma with an electrode to deliver an anionic, hydrophilic dye into the cytoplasm under a low-voltage current, enabling the dye to diffuse and label the soma and branches. Confocal microscopy is then used to visualize the...

Source: Jongbloets, B. C., et al. Visualizing Protein Kinase A Activity In Head-fixed Behaving Mice Using In Vivo Two-photon Fluorescence Lifetime Imaging Microscopy. J. Vis. Exp. (2019) This video demonstrates a two-photon fluorescence lifetime imaging microscopy procedure for visualizing protein kinase A activity in head-fixed, behaving mice during enforced locomotion.

Source: Kwon, J., et al., Spectral Reflectometric Microscopy on Myelinated Axons In Situ. J. Vis. Exp. (2018) This video demonstrates the use of spectral reflectometry with a hyperspectral confocal microscope to analyze interference patterns and determine myelinated axon diameters in fixed brain tissue slices.

Begin with a patient with meningioma, or a brain tumor, positioned in an MRI scanner for non-invasive brain imaging.Adjust the scanner to obtain structural images of individual slices of the brain.Enhance the contrast to improve tissue differentiation.Use interslice magnetization transfer ratio imaging on brain slices using radiofrequency pulses slightly offset from the MRI signal.The pulses deliver energy to the proton pool in macromolecules and bound water molecules.This energy transfers to...

Source: Liau, E. S. et al. Visualization of Motor Axon Navigation and Quantification of Axon Arborization In Mouse Embryos Using Light Sheet Fluorescence Microscopy. J. Vis. Exp. (2018). This video demonstrates the use of light sheet fluorescence microscopy to image motor neuron projections and axon branching in transgenic mouse embryos. It outlines the steps involved in sample preparation, imaging, and 3D reconstruction of axonal branching for assessing motor neuron growth and connectivity.

Quantitative susceptibility mapping, or QSM, quantifies the magnetic susceptibility of brain tissue, which reflects its cellular composition, like myelin content.Begin by acquiring ex-vivo magnetic resonance imaging or MRI data of a fixed human brain hemisphere.Use 3D gradient magnetic fields to magnetize the tissue and collect signals at multiple time points or echoes to reduce background noise and artifacts and enhance the signals.Generate phase maps for all echoes, ensuring the removal of...

Source: Feng, Y., et al. Viscoelastic Characterization of Soft Tissue-Mimicking Gelatin Phantoms using Indentation and Magnetic Resonance Elastography. J. Vis. Exp. (2022) This video demonstrates the method of magnetic resonance elastography (MRE) for assessing tissue viscoelastic properties by analyzing shear wave propagation through a gelatin phantom, mimicking brain tissue. The process involves generating and capturing shear waves with magnetic resonance imaging or MRI and analyzing wave...

Source: Boyer, N. P. et. al., Imaging and Analysis of Neurofilament Transport in Excised Mouse Tibial Nerve. J. Vis. Exp. (2020) This video demonstrates the fluorescence photoactivation method to analyze neurofilament transport in myelinated axons of peripheral nerves. By tracking photoactivated green fluorophore-tagged neurofilaments, the technique provides insights into axonal transport in neurodegenerative diseases.

Source: Kulkarni, M. et al. Imaging Ca2+ Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina. J. Vis. Exp. (2015)This video demonstrates the use of two-photon microscopy to monitor calcium dynamics in cone photoreceptors of a transgenic mouse retina. It outlines the steps for preparing retinal slices, imaging FRET-based calcium biosensors, and analyzing fluorescence changes to quantify calcium levels under background illumination and light stimulation.

Source: Nishidate, I., et al. Simultaneous Evaluation of Cerebral Hemodynamics and Light Scattering Properties of the In Vivo Rat Brain Using Multispectral Diffuse Reflectance Imaging. J. Vis. Exp. (2017)This video demonstrates the use of multispectral diffuse reflectance imaging to analyze cerebral blood flow, oxygen levels, and tissue structure changes in an anesthetized rat, providing insights into brain hemodynamics and morphology under varying conditions.

Source: Van Wonterghem, E., et al. Microdissection and Whole Mount Scanning Electron Microscopy Visualization of Mouse Choroid Plexus. J. Vis. Exp. (2022)This video demonstrates the preparation and imaging of choroid plexus tissue from a mouse brain using scanning electron microscopy (SEM). The process includes tissue fixation, dehydration, and coating with a conductive platinum layer to stabilize and prepare the sample for imaging. SEM captures detailed images of epithelial cells with...

Source: Kato, D. et. al., Evaluation and Manipulation of Neural Activity Using Two-Photon Holographic Microscopy. J. Vis. Exp. (2022)This video demonstrates the two-photon imaging technique combined with optogenetics using holographic microscopy. Using a spatial light modulator, this technique enables precise neuronal stimulation expressing the red-light-sensitive protein and calcium imaging with minimal photodamage. This approach provides insights into the functional connectivity and...

Source: Canovic, E. P., et al. Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry. J. Vis. Exp. (2016)This video demonstrates the use of atomic force microscopy (AFM) to measure the viscoelastic properties of brain tissue, where a cantilever with a spherical probe interacts with the tissue and bends under applied forces. A laser beam deflected onto a detector tracks the cantilever to measure indentation depth and...

Source: Canovic, E. P., et al. Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry. J. Vis. Exp. (2016)In this video, a rheometer was used to apply controlled oscillatory rotational motion to brain tissue to generate shear strain and evaluate the tissue's viscous and elastic properties. The rheometer, as a functional tool, it provides insights into brain mechanics during injury or neurodegenerative diseases.

Source: Hare, D. J., et.al. Imaging Metals in Brain Tissue by Laser Ablation - Inductively Coupled Plasma - Mass Spectrometry (LA-ICP-MS). J. Vis. Exp. (2017)This video demonstrates the use of laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) to visualize and quantify metal distributions in mouse brain tissue. The protocol involves laser ablation to generate an aerosol of sample particles, ionization of the particles in high-temperature plasma, and mass spectrometry to...

Source: Piazza, V., et al., Label-Free Non-Linear Optics for the Study of Tubulin-Dependent Defects in Central Myelin. J. Vis. Exp. (2023)This video demonstrates the procedure for imaging microtubule abnormalities in a rat brain tissue slice using a two-photon excitation microscope. It employs second harmonic generation (SHG) signals to detect tubulin defects and reduced myelin production.

Source: Daniele, F., et. al TIRFM and pH-sensitive GFP-probes to Evaluate Neurotransmitter Vesicle Dynamics in SH-SY5Y Neuroblastoma Cells: Cell Imaging and Data Analysis. J. Vis. Exp. (2015).This video demonstrates the imaging of human neuroblastoma cells using a total internal reflection fluorescence (TIRF) microscope to visualize fluorophore-tagged synaptic vesicles. The cells are first focused in epifluorescence mode. Adjustments are then made to achieve total internal reflection,...

Source: Winkle, C. C., et al. Utilizing Combined Methodologies to Define the Role of Plasma Membrane Delivery During Axon Branching and Neuronal Morphogenesis. J. Vis. Exp. (2016)This video demonstrates total internal reflection fluorescence (TIRF) microscopy for visualizing exocytic events in cortical neurons. A pH-sensitive green fluorescent protein (GFP) marker fluoresces upon vesicle fusion, with selective TIRF excitation capturing membrane-proximal exocytosis in time-lapse imaging.

Source: McCullagh, E. A., et al. Coherent Anti-Stokes Raman Spectroscopy (CARS) Application for Imaging Myelination in Brain Slices. J. Vis. Exp. (2022)The video demonstrates fluorescence and Coherent Anti-Stokes Raman Spectroscopy (CARS) imaging to visualize neuronal architecture in rodent brain tissue. Nissl staining labels cell bodies by binding to ribosomal RNA, while CARS imaging targets lipid-rich myelin through laser-induced signals. Overlaying the fluorescence and CARS images provides a...

Source: Hontani, Y., et al. Deep-Tissue Three-Photon Fluorescence Microscopy in Intact Mouse and Zebrafish Brain. J. Vis. Exp. (2022)This video demonstrates the setup and execution of three-photon imaging in an anesthetized zebrafish brain. The protocol enables deep-tissue visualization of fluorescently labeled neurons, revealing real-time neuronal activity and structures for neuroscience research applications.