Manual Segmentation

Manual segmentation is the process of identifying and outlining anatomical structures, lesions, or other regions of interest in medical images. A trained user reviews image slices and delineates boundaries by assigning pixels or three-dimensional voxels to specific labels, using visual features such as intensity, shape, and tissue contrast. The resulting annotations support quantitative measurements of volume, size, and shape, and can guide diagnosis, treatment planning, and disease monitoring. Manual segmentation also provides reference data for evaluating automated image-analysis methods and training machine-learning models, although its accuracy can depend on the operator’s expertise and the clarity of the image.

Manual Segmentation - Related Videos

Research

JoVE Journal - Neuroscience

A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures

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Cited by 33 •

2014

The present work provides a comprehensive set of guidelines for manually tracing the medial temporal lobe (MTL) structures. This protocol can be applied to research involving structural and/or combined structural-functional magnetic resonance imaging (MRI) investigations of the MTL, in both healthy and clinical groups.

Manual Segmentation of the Human Choroid Plexus Using Brain MRI

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Cited by 13 •

2023

Despite the crucial role of the choroid plexus in the brain, neuroimaging studies of this structure are scarce due to the lack of reliable automated segmentation tools. The present protocol aims to ensure gold-standard manual segmentation of the choroid plexus that can inform future neuroimaging studies.

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

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Cited by 9 •

2015

The goal of this manuscript is to study the hippocampus and hippocampal subfields using MRI. The manuscript describes a protocol for segmenting the hippocampus and five hippocampal substructures: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum.

Education

JoVE Science Education - Basic Biology

Rabbit Handling and Manual Restraint

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2026

All animal procedures described here must be conducted in accordance with institutional animal ethics guidelines and approved by IACUC. All procedures must follow the principles of the 3Rs—Replacement, Reduction, and Refinement—and must be performed by trained personnel. Rabbits possess powerful hindlimb musculature and are susceptible to spinal injury if they struggle or kick while inadequately supported. Because rabbits vary in temperament and may struggle during restraint, handlers should...

Research

JoVE Journal - Biology
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Volume Segmentation and Analysis of Biological Materials Using SuRVoS (Super-region Volume Segmentation) Workbench

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Cited by 10 •

2017

Segmentation of three-dimensional data from many imaging techniques is a major bottleneck in analysis of complex biological systems. Here, we describe the use of SuRVoS Workbench to semi-automatically segment volumetric data at various length-scales using example datasets from cryo-electron tomography, cryo soft X-ray tomography, and phase contrast X-ray tomography techniques.

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