Volumetric Brain Scanning
Volumetric Brain Scanning - Related Videos
07:34
Delivery of Antibodies into the Brain Using Focused Scanning Ultrasound
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Cited by 6 •
2020
Presented here is a protocol to transiently open the blood-brain barrier (BBB) either focally or throughout a mouse brain to deliver fluorescently-labeled antibodies and activate microglia. Also presented is a method to detect the delivery of antibodies and microglia activation by histology.
07:47
Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy
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Cited by 32 •
2016
Mitochondrial visualization and analysis from mammalian brain tissue is a challenging task. Here, we describe how three dimensional (3D) reconstruction analysis from the serial block-face scanning electron microscopy (SBFSEM) can be used to gain insights on the morphological and volumetric analysis of this critical energy generating organelle.
02:23
Visualization of a Mouse Brain Choroid Plexus Using Scanning Electron Microscopy
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2025
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...
08:57
Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue
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Cited by 105 •
2011
This protocol describes how resin embedded brain tissue can be prepared and imaged in the three dimensions in the focussed ion beam, scanning electron microscope.
12:50
Lesion Explorer: A Video-guided, Standardized Protocol for Accurate and Reliable MRI-derived Volumetrics in Alzheimer's Disease and Normal Elderly
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Cited by 29 •
2014
Lesion Explorer (LE) is a semi-automatic, image-processing pipeline developed to obtain regional brain tissue and subcortical hyperintensity lesion volumetrics from structural MRI of Alzheimer's disease and normal elderly. To ensure a high level of accuracy and reliability, the following is a video-guided, standardized protocol for LE's manual procedures.
FAQs
Registration places images into a comparable spatial framework, while segmentation separates anatomical structures within the reconstructed volume. Together, these processing stages make it possible to calculate regional measurements consistently rather than relying on visual inspection of individual slices. In neuroscience research, that consistency supports comparisons among people and assessment of structural change across repeated imaging sessions.
Segmentation is central because volumetric measurements depend on identifying which parts of the brain belong to each structure or tissue distribution. Once regions are distinguished, researchers can calculate their volumes and examine regional size or shape. The resulting measurements provide a quantitative basis for studying differences associated with development, aging, neurodegenerative disease, or injury.
Three-dimensional analysis adds information that a single slice cannot provide: it permits assessment of regional size, shape, and tissue distribution across the full reconstructed structure. This matters when structural differences are distributed through a region rather than visible in one section. The approach therefore supports quantitative anatomical comparisons instead of conclusions based only on visual appearance.
Researchers begin with high-resolution magnetic resonance images, reconstruct them into a three-dimensional volume, register images so they can be compared, and segment structures for measurement. The workflow ends with calculated regional volumes and related anatomical measurements. These outputs can then be compared across individuals or across time to investigate structural differences or change.
It is useful when the research question concerns structural change, including brain development, aging, neurodegenerative disease, injury, or treatment effects. Quantitative regional measurements can help investigators characterize disease mechanisms, evaluate possible biomarkers, and examine whether anatomy changes during a longitudinal study. Its value lies in converting anatomical images into measurements suitable for systematic comparison.
Comparing measurements from repeated imaging over time can reveal changes in regional brain volumes, shape, or tissue distribution. Such comparisons help distinguish a one-time anatomical difference from a pattern of structural change and can support studies of disease progression or treatment effects. The measurements are therefore useful for tracking outcomes, not only describing anatomy at a single time point.