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This free code is an ImageJ plugin that allows one to count the number of synapses of a neuron.

This plugin, is a joint work between the team "Structural Synaptic Plasticity" of SpineUp and "Programming and Symbolic Computation Team” of University of La Rioja.


Gadea Mata Martínez (gadea.mata at gmail dot com or gadea.mata at unirioja dot es)


Synapses are the points of connection between neurons. The relevance of synapses comes from the fact that they are related to the computational capabilities of the brain. The possibility of changing the number of synapses may be an important asset in the treatment of neurological diseases, such as Alzheimer. This plugin provides a semi-automatic method for counting synapses. This tool needs two images which are obtained using laboratory techniques. The images are obtained from the same neuron in a concrete moment using two antibody markers: bassoon and synapsin.


Last Version (January 2016):

Download SynapCountJ v2.jar (Update SynapCountJ v2.0 January 2016)

Download user manual:

Manual SynapCountJ (english)

Manual SynapCountJ (castellano)

Second Version (September 2012):

Download SynapCountJ v1.1 (Update SynapCountJ v1.0 September 2011)

Download user manual:

Manual SynapCountJ v1 (english)

Manual SynapCountJ v1 (castellano)

First Version (May 2011):

Download SynapCountJ

Download Manual SynapCountJ.pdf


The program is open source; you can redistribute is and/or modify it under the terms of the GNU General public License.


We truly hope that this program is useful, but WITHOUT ANY WARRANTY. Feel free to improve or adjust it for your needs.

plugin/utilities/synapsescountj/start.txt · Last modified: 2019/04/12 13:13 by

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