neuTube is an open source software for reconstructing neurons from fluorescence microscope images. It has a nice interactive system. It has 3D viewer, which can be clicked in 3D and perform neuron tracing semi-automatically. It can automatic recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages.
neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.
Source Code available at: https://github.com/janelia-flyem/NeuTu