Manually counting synapses

I have to manually count synapses/varicosities of a neuron through an image stack and I was wondering how others have been doing this?
(I’ve heard of synapcountj but for my specific project I cannot use this.)

And more specifically, I have to find a way to count the synapses and keep track by marking the images themselves within the image stack. The way I’ve been counting the synapses thus far is by first tracing the neurons and then using the path list to keep track of the synapses I’ve counted but my mentor would like me to find a way to mark the synaptic vesicles on the images of the neuron to show the distribution of the synapses. Is there a way to do this? I’d really appreciate any suggestions, I’m open to using other software but I just need to find a way to do it.

Thank you in advance.


Hello Dianne,

Have you tried using the Cell Counter?


ImageJ’s multi-point tool has also gotten quite good now. See also this forum post and this one and this one for related discussion.

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