Our programs are open source; you can redistribute are and/or modify them under the terms of the GNU General public License.


We truly hope that these program are useful, but WITHOUT ANY WARRANTY. Feel free to improve or adjust them for your needs.


Suggestion can be sent to:

gadeamata at spineup dot es or gadea dot mata at unirioja dot es


You can find our ImageJ/Fiji plugins here:



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 (May 2016):

upload: now the plugin shows a ROI manager window with the points where the synapses are.

Manual SynapCountJ in English
Documento Adobe Acrobat 800.3 KB
Manual SynapCountJ in Spanish
Documento Adobe Acrobat 615.2 KB

Previous Versions:

Download SynapCountJ_v2.zip (January 2016)

Author: Gadea Mata Martínez
Archivo comprimido 54.9 KB


The theory of zigzag persistence has been used to develop this plugin.


NeuronZigZagJ calculates the main structure and allows one to check automatically whether two dendrites that are linked in the maximal projection of the stack are really the same, or are overlapped on the plane but there is no intersection between them in the space.


Download NeuronZigZagJ_.zip, and unrar. Put NeuronZigZagJ_.jar to the plugins folder or subfolder. Restart ImageJ (or Fiji) or click “Refresh Menu”, which is at Help Menu, and the plugin “NeuronZigZagJ_” command will be located at Menu/Plugins.


Author: Gadea Mata Martínez
Archivo comprimido formato ZIP 31.6 KB


NucleusJ is a software system designed to the identification and quantification of neurons from immunofluorescence images. The underlying algorithms of this program are based on homological  and geometrics methods for digital imaging.

This plugin has been implemented in Java for the system ImageJ / Fiji and can be executed in Windows (XP/Vista/7), Mac OS X and Linux.


This plugin and the preprocess of images have been run in an Intel Core i7 3.07GHz computer with 24 GB of memory, with a graphic card of nVidia Corporation GF110 (GeForce GTX 560 Ti) under the Ubuntu Linux operating system 11.10.


NucleusJ employs different mathematical algorithms. Due to this reason, the first window is to configure the settings related for example with the continuity of image information, like the radio for median filter. The other parameters are related to the algorithms for discriminating the neuronal nucleus from the other ones, like the maximum and minimum size of all nucleus or only neuronal nucleus.


NucleusJ processes the two images (nucleus and neurons image) and the first result is the number of total nucleus (astrocytes and neurons are included) present in the picture.


Selection of neuronal nucleus is done  by thresholding.


With this value, the plugin runs and returns an image with the neuronal nucleus selected.
The window named “ROI Manager” allows the user to modify and correct the final result.
Manual will be available soon.
Download NucleusJ_12.rar (http://spineup.jimdo.com/downloads/), and unrar. Put NucleusJ_v12.jar into the plugins folder or subfolder. Restart ImageJ (or Fiji) or click “Refresh Menu”, which is at Help Menu. The plugin “NucleusJ_v12” command will be located at Menu/Plugins.
NucleusJ_v12.rar (Sep 2013)
Archivo comprimido 50.9 KB
Manual NucleusJ in English
Documento Adobe Acrobat 1.0 MB


This plugin implement a method to detect the neuronal structure from image (in the example, images of hippocampal neuron in culture, transfected with Actin-GFP).

This method can be split into two steps, the first one process the image with filters to dismiss the elements which are not part of the structure of the main neuron, and the second one is based in the persistent homology. This is a technique which allows one to study the lifetimes of topological attributes.


Download neuronpersistent.rar, and unrar. Put neuronpersistentj_.jar to the plugins folder or subfolder. Restart ImageJ (or Fiji) or click “Refresh Menu”, which is at Help Menu, and the plugin “NeuronPersistentJ” command will be located at Menu/Plugins.


NeuronPersistentJ_v1.rar (Last Version May 2013)
Authors: Rubén Saénz Francia and Gadea Mata Martínez
Archivo comprimido 7.1 KB
NeuronPersistentJ.rar (First Version July 2012)
Author: Gadea Mata Martínez
Archivo comprimido 5.5 KB

Save All

This plugin save all and close the opened images in the selected folder. If the image is a stack, the plugin separate each slices in a new image, and save each slice like a new image, in addition creates the Z projection from stack and saves it.


Download SaveAll_.jar. Put SaveAll.jar to the plugins folder, or subfolder, restart ImageJ / Fiji or refresh menu (Help → 'Refresh Menu') , and there will be a new “SaveAllImages” command in the Plugins menu, or submenu.

Last Update: January 2014
Archivo comprimido formato ZIP 9.5 KB