Problems w/ SNT, skeletonizing

Recently I’ve had issues analyzing traced .swc files, and issues are visible when skeletonizing. After importing (e)swc’s onto corresponding .tif’s, and selecting ‘Filters for Visibility of Paths (2)’, nearly all of the paths become highlighted at the beginning of the image stack - even if they are not attached to the stalk/main path until later in the stack.

After skeletonizing the main path (and subsequently merging with a skeleton of branching paths), a related issue occurs. All paths appear in the beginning of the composite image stack, and the main path/stalk appears elongated in these few stack images, rather than as a single point.

I have analyzed multiple images and this hasn’t occurred. I have tried rescaling the .tif files, and going back into SNT to make sure the traces are accurate, but beyond this I’m not sure why it is occurring.

Attached: Z projects of traces
Red/yellow = stalk
Green = branches/processes

Screen Shot 2021-04-09 at 12.09.34 AM
Normal stalk

Elongated stock

@CJCmcbucb, Sorry I cannot understand issue. What is the problem exactly? Imported paths are not associated with the right z-plane? Nodes are shifted/translated in the Z dimension?

Why the subsequent merge? You should be able to select the paths that you need to skeletonize and the Analyze → Skeletonize… command in the Path Manager should process only those selected.