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Updated: Jun 24, 2026
Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells
Published on: October 10, 2015
Spot Spine, a freely available ImageJ plugin for 3D detection and morphological analysis of dendritic spines
Jean-Francois Gilles1, Philippe Mailly2, Tiago Ferreira3
1Institut de Biologie Paris Seine, CNRS, Sorbonne Universite, Paris, Île-de-France, France.
Background:
Dendritic spines are tiny protrusions found along the dendrites of neurons, and their number is a measure of the density of synaptic connections. Altered density and morphology is observed in several pathologies, and spine formation as well as morphological changes correlate with learning and memory. The detection of spines in microscopy images and the analysis of their morphology is therefore a prerequisite for many studies. We have developed a new open-source, freely available, plugin for ImageJ/FIJI, called Spot Spine, that allows detection and morphological measurements of spines in three dimensional images.
Method:
Local maxima are detected in spine heads, and the intensity distribution around the local maximum is computed to perform the segmentation of each spine head. Spine necks are then traced from the spine head to the dendrite. Several parameters can be set to optimize detection and segmentation, and manual correction gives further control over the result of the process.
Results:
The plugin allows the analysis of images of dendrites obtained with various labeling and imaging methods. Quantitative measurements are retrieved including spine head volume and surface, and neck length.
Conclusion:
The plugin and instructions for use are available at https://imagej.net/plugins/spot-spine.
