Three-dimensional Brain Models

Three-dimensional brain models are laboratory systems that reproduce selected structural and cellular features of the brain in a spatially organized format, helping researchers study nervous-system development and disease. They are commonly generated from neural stem cells or pluripotent stem cells, which differentiate into neuronal and glial populations and can self-organize within supportive culture conditions or biomaterials. These models include brain organoids, engineered neural tissues, and region-specific cultures used to investigate cell interactions, gene function, neurodevelopmental disorders, infection, and drug responses. By complementing animal studies and conventional two-dimensional cultures, three-dimensional brain models provide a more physiologically relevant platform for neuroscience research while enabling controlled experimental manipulation.

Three-dimensional Brain Models - Related Videos

Research

JoVE Journal - Neuroscience

Three-Dimensional Shape Modeling and Analysis of Brain Structures

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Cited by 2 •

2019

We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images.

High-Resolution Three-Dimensional Confocal Imaging of the Blood-Brain Barrier in a Mouse Brain Section

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2025

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...

Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury

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Cited by 51 •

2013

A way to gain new insights into the complexity of the brain inflammatory response is presented. We describe immunofluorescence-based protocols followed by three-dimensional confocal analysis to investigate the pattern of co-expression of microglia/macrophage phenotype markers in a mouse model of focal ischemia.

Three-Dimensional Visualization of a Rabies Virus Infection in Mouse Brain Tissue

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2025

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...

Real-Time Gene Expression Monitoring in Brain Slices via Three-Dimensional Imaging

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2025

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.

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