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Related Concept Videos

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Confocal Fluorescence Microscopy

Confocal microscopy is an advanced microscopic technique. The prime advantage of the confocal microscope over other microscopy techniques is its ability to block the out-of-focus light from the illuminated samples using pinholes. It is widely used with fluorescence optics to obtain high-resolution, sharp contrast images. Unlike optical microscopes, confocal microscopes use a focused beam of light laser to scan the entire sample surface at different z-planes. These microscopes are, therefore,...
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DUSP5 Downregulation in Nucleus Accumbens Core Correlates with Cocaine-Induced Maladaptive Synaptic Plasticity.

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Related Experiment Video

Updated: Jun 17, 2026

Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury
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Characterizing Microglial Morphology: Methodological Advances in Confocal Imaging and Analysis.

Juan P Taborda-Bejarano1, David B Nowak1,2, Fernando Chaure1

  • 1Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.

Cells
|September 13, 2025
PubMed
Summary

This study presents a standardized imaging pipeline for analyzing microglia morphology in the nucleus accumbens core. CellSelect-3DMorph offers a rapid, open-access alternative for high-throughput microglial analysis.

Keywords:
analysismicrogliamorphologyneuroimmune

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Quantifying Microglia Morphology from Photomicrographs of Immunohistochemistry Prepared Tissue Using ImageJ
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Area of Science:

  • Neuroscience
  • Immunology
  • Cell Biology

Background:

  • Microglia, the immune cells of the brain, exhibit dynamic changes in structure and function during stress, addiction, and in response to pharmacological treatments.
  • While molecular assays offer insights, morphological analysis is crucial for understanding region-specific microglial responses, yet requires standardized methods.

Purpose of the Study:

  • To establish a standardized imaging pipeline for analyzing microglia morphology in the nucleus accumbens core (NAcore).
  • To compare the utility and output of IMARIS and CellSelect-3DMorph platforms for quantifying microglial morphology.
  • To demonstrate the application of morphological data in identifying distinct microglial subpopulations.

Main Methods:

  • Developed a standardized confocal imaging pipeline for NAcore microglia with precise anatomical referencing.
  • Compared IMARIS and CellSelect-3DMorph for microglial morphology quantification after adenosine triphosphate (ATP) treatment.
  • Utilized principal component analysis (PCA) clustering on software-derived morphological parameters.

Main Results:

  • Both IMARIS and CellSelect-3DMorph reliably quantified microglial morphological features, including those affected by ATP treatment.
  • CellSelect-3DMorph demonstrated a faster, open-access workflow suitable for high-throughput analysis.
  • PCA clustering effectively identified distinct microglial subpopulations based on morphology.

Conclusions:

  • The developed pipeline provides a practical framework for reproducible microglial morphological analysis.
  • CellSelect-3DMorph serves as a valuable, rapid, and accessible tool for high-throughput microglial studies.
  • Morphological analysis, complemented by advanced data processing, aids in discerning functional microglial states.