I don't think something like this exists for the standard ImageJ distribution. Only the NeuronJ plugin exists for ImageJ and it is a planar 2D image application.

The FIJI fork of ImageJ does have something like this. FIJI stands for Fiji Is Just ImageJ. It is a platform that has expanded widely on the ImageJ platform. The Simple Neurite Tracer does have a 3D mode that may be useful for your reconstruction. You can fid the software at http://fiji.sc and the Simple Neurite Tracer at http://fiji.sc/wiki/index.php/Simple_Neurite_Tracer .

Thanks for your answer H. Morris, I will look into it.

Justyna,

The simple neurite tracer plugin mentioned by H Morris is quite good. It is, however, intended to trace neurons. Your question did not specify if you were more interested in connectivity/tracing or morphologic reconstruction.

I highly recommend Fiji. You can use the 3D viewer plugin to visualize the volumetric and surface reconstruction data. Simple neurite plugin can be used to trace neurons in 2D and 3D. TrakEM2 can also be used to trace neuronal processes with the added advantage of keeping the actual morphology. Look into areatree for both and arealist for morphology only.

For a better response, clarify your analytic purpose and input imagery. With that information, we can help you better.

Hi Kristopher, thanks for your reply. I would like to trace input connectivity to a single neuron I tagged during electrophys recordings.

Try TrakEM2 then. You can use treelines and add connections with directionality.