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Related Experiment Video

Updated: May 3, 2026

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization
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Isolating specific cell and tissue compartments from 3D images for quantitative regional distribution analysis using

Keith K Fenrich1, Ethan Y Zhao2, Yuan Wei2

  • 1CIHR Group in Sensory-Motor Integration, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6; Center for Neuroscience Studies, Queen's University, Kingston, ON, Canada K7L 3N6; Aix Marseille University, Developmental Biology Institute of Marseille-Luminy (IBDML), CNRS 7288, Case 907 - Parc Scientifique de Luminy, 13009 Marseille, France; Faculty of Rehabilitation Medicine, University of Alberta, 3-88 Corbett Hall, Edmonton, AB, Canada T6G 2G4.

Journal of Neuroscience Methods
|February 4, 2014
PubMed
Summary

We developed Grow and Shrink Volumes of Interest (GSVI) algorithms to isolate cellular compartments in 3D images. This open-source tool enables quantitative analysis of tissue and cell distributions for research.

Keywords:
Image analysisIntravital microscopyMembrane proteinsOpen-source

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Area of Science:

  • Neuroscience
  • Cell Biology
  • Biomedical Imaging

Background:

  • Quantitative analysis of cellular and tissue compartments in 3D image stacks is vital for understanding physiology.
  • Existing methods for isolating specific regions are limited, often requiring proprietary software.

Purpose of the Study:

  • To develop an open-source, user-friendly algorithm for isolating cellular and tissue compartments from 3D image stacks.
  • To overcome limitations of current methods in mapping distributions within complex biological structures.

Main Methods:

  • Developed Grow and Shrink Volumes of Interest (GSVI) algorithms for isolating specific cellular and tissue compartments.
  • Integrated GSVI algorithms into a free, open-source, user-friendly computer program.
  • Applied GSVI to isolate perivascular regions in vivo and cell membrane regions in fixed tissue.

Main Results:

  • Successfully isolated perivascular regions in live animal cortex and cell membrane regions of spinal motoneurons.
  • Tracked real-time biodistribution of fluorophores with sub-cellular resolution after vascular microlesion.
  • Mapped distributions of KCC2 and gephyrin immunolabeling in neuronal compartments.

Conclusions:

  • GSVI algorithm enables quantification of regional biomarker differences and their relation to cell function.
  • The tool facilitates studying therapeutic effects on biomolecule and cell redistribution in diseased tissues.