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Updated: Apr 5, 2026
An Analytical Tool that Quantifies Cellular Morphology Changes from Three-dimensional Fluorescence Images
Published on: August 31, 2012
Protocol to study synapse density or volume-SynDOVE-in brain using confocal microscopy and Imaris three-dimensional
Nolwazi Z Gcwensa1, Khaliah Y Long2, Arielle F Manabat2
1Killion Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
Abstract:
We present a protocol for analyzing pre- and postsynaptic loci in fixed brain sections using confocal microscopy images and Imaris software. We describe steps for capturing z stack images of immunofluorescent-labeled synaptic proteins using a confocal microscope. We then detail procedures for deconvolving images, rendering three-dimensional (3D) surface reconstructions of synaptic markers, and isolating closely juxtaposed pre- and post-synaptic 3D surfaces, herein termed "synaptic loci." This protocol allows for quantitation of synaptic loci density, as well as pre- and postsynaptic volumes. For complete details on the use and execution of this protocol, please refer to Gcwensa et al.1.
