Using NeuronJ with Fiji on Mac OS

Hello everyone!

Due to my studies of Medicine, I am recently working on a science Project, which requires evaluating the effect of a certain substance on the synaptogenesis of hippocampal rat cells.

I have collected a huge amount of data, more specific photos of my neurons which now need to be evaluated - their synapses need to be counted.
I wanted to use the NeuronJ Plugin for Fiji but there have been two major problems to it, which is why I need your help!

  1. After installing the Plugin NeuronJ and colouring my dendrits the manuel wants me to open a Plugin called “SynapCountJ”, but I cannot find a working download link (or even the named Plugin under “Plugins” in Fiji.

  2. In order to compare the different number of synapses, I somehow need to measure the same length of every dendrite - I have no idea how to do so as there is no way of marking a certain area (of the dendrite) and measure at the same time.

I´d be thrilled about some help!

Best regards


Dear Cindy,

I recently downloaded he SynapCountJ plugin successfully from the related ImageJ Documentation wiki available here:
Once you have downloaded the [SynapCountJ v2.jar] file , move it to the plugins folder of your ImageJ installation (

You might also want to have a look at SynQuant (available here:; related publication: and at the Simple Neurite Tracer plugin to trace your neurons (

SynQuant can detect and measure neurites as well and generates normalised outputs, e.g. synapses per length of neurite. The Simple Neurite Tracer also has easy options to measure the length of neurites.

Hope this helps,