Morphological Analysis Software

Morphological analysis software is a class of digital tools that extracts and quantifies the shape, size, and spatial organization of structures from images, making complex biological form measurable and comparable. In neuroscience, it typically processes microscopy images through preprocessing, segmentation, feature detection, and quantitative measurement, separating cellular or tissue structures from background and calculating descriptors such as length, branching, area, or volume. Researchers use these workflows to examine neuronal morphology, dendritic architecture, axonal organization, and changes in brain tissue across development, disease models, or experimental conditions. By standardizing image-based measurements, the software supports reproducible analyses, reduces manual scoring, and helps connect structural changes with neural function and pathology.

Morphological Analysis Software - Related Videos

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JoVE Journal - Neuroscience
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Mapping Microglial Parameters Software (MMPS): An Open-Source, User-Friendly Tool for Quantitative Microglia Morphology Analysis

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2026

Mapping Microglial Parameters Software (MMPS) is a user-friendly analysis pipeline that requires no coding expertise and semi-automates single-cell microglial morphology analysis from immunofluorescence images. Validated in a rodent lipopolysaccharide-induced neuroinflammation model, MMPS reproducibly detects activation-associated morphological changes and enables standardized, scalable microglial phenotyping.

Research

JoVE Journal - Biology
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Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects

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Cited by 154 •

2010

Tomato Analyzer (TA) quantifies attributes of two dimensional shapes and color in a reproducible and accurate manner. A step-by-step procedure for obtaining high quality digitalized images of tomato fruit, morphological and color analyses of these images and several applications using the data generated through this software are described.

Research

JoVE Journal - Neuroscience
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Automated Analysis of C. elegans Swim Behavior Using CeleST Software

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Cited by 18 •

2016

An efficient and simple methodology for computer-based analysis of nematode swimming behavior in liquid is described. The method requires little to no investment for C. elegans laboratories. The hardware used is standard, and the computer software for the behavioral analysis (CeleST) is an open source one.

Research

JoVE Journal - Neuroscience

Analysis of Dendritic Spine Morphology in Cultured CNS Neurons

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Cited by 69 •

2011

Numerous recent studies have identified mutations in synaptic proteins associated with brain pathologies. Primary cultured cortical neurons offer great flexibility in examining the effects of these disease-associated proteins on dendritic spine morphology and motility.

Automated Sholl Analysis of Digitized Neuronal Morphology at Multiple Scales

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Cited by 61 •

2010

We have developed a computer program to analyze neuronal morphology. In combination with two existing open source analysis tools, our program performs Sholl analysis and determines the number of neurites, branch points, and neurite tips. The analyses are performed so that local changes in neurite morphology can be observed.

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