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Updated: Nov 23, 2025

Quantifying Synapses: an Immunocytochemistry-based Assay to Quantify Synapse Number

Quantifying Synapses: an Immunocytochemistry-based Assay to Quantify Synapse Number

Published on: November 16, 2010

SynapsEM: Computer-Assisted Synapse Morphometry.

Shigeki Watanabe^1,2, M Wayne Davis³, Grant F Kusick¹

¹Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.

Frontiers in Synaptic Neuroscience

|January 4, 2021

Summary

This summary is machine-generated.

SynapsEM is a new computer program that automates synaptic morphometry. This tool accelerates the analysis of synaptic structure, enabling more comprehensive studies of neuronal function.

Keywords:

SynapsEM electron microscopy morphometry synapse ultrastructural analysis

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Last Updated: Nov 23, 2025

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Area of Science:

Neuroscience
Cell Biology
Biophysics

Background:

Synaptic structure is critical for function.
Analyzing synaptic ultrastructure via electron microscopy requires complex morphometry.
Current methods are time-consuming and labor-intensive.

Purpose of the Study:

To develop a custom computer program, SynapsEM, for efficient and comprehensive synaptic morphometry.
To automate the quantification of key structural features at synapses.

Main Methods:

Developed ImageJ/Fiji macros to segment synaptic structures and record coordinates.
Exported coordinates as text files for reexamination.
Created a Matlab program to calculate synaptic parameters from coordinates.

Main Results:

SynapsEM automates the quantification of vesicle and organelle size, number, density, and spatial relationships.
The program allows for extraction of advanced parameters, such as docked vesicle locations.
Analysis is accelerated, enabling studies on hundreds to thousands of images.

Conclusions:

SynapsEM significantly accelerates synaptic morphometry.
The program promotes more comprehensive analysis of synaptic ultrastructure.
This tool facilitates deeper understanding of structure-function relationships in synapses.