Hi, Sumeer

Are these z stacks from physically sectioned slices? If not, are there overlap between them?

If there is not overlap between stacks in Z direction, you can:

1st. Do the reconstruction within each stack to generate SWC file (using any reconstructions algorithm in Vaa3D or Right Click Tool in Vaa3D 3D view);
2nd. Use Plugin>neuron_stitch>auto/live_stitch_neuron_SWC to stich the reconstruction in adjacent stacks.

This will give you a complete reconstruction. But currently the image cannot be stitched in this way. I am working an extension of the tool to allow stitch images as well.

Hanbo