Different programs and different parameters may lead to different results (i.e. various # of reconstruction nodes, etc), of course.

In Vaa3D-Neuron result, multiple segments may be saved in the same swc file. This is NOT a bug, indeed, this makes it is more flexible and powerful to save any reconstruction.

But suppose you have a connect tree in the reconstruction, and the segments have been saved separately, and you want to eliminate the -1's. You can go to Vaa3D and right-click the neuron in a 3D viewer, and from the pop-up menu select "join all neuron segments and remove redundant nodes".

Note, if you directly drag and drop a swc file into Vaa3D, without having an image, you can directly open it in the 3D viewer. But when you right click, you will have to select "Edit the neuron", which will decompose the neuron structure first. And then when you right click the neuron again, you will see the "join all neuron segments and remove redundant nodes" pop-up menu-item.

-Hanchuan


Originally posted by Jesús Pujol: