@ihertzler, SNT parses 8-, 16-, and 32-bit images the same way and the date is cached internally when the image is loaded. Bit-depth should be irrelevant to any issues you are having.
One thing that could make a difference is if you are inverting your image somehow which you may not realize if, e.g., you are using and inverted LUT. That being said, I can trace your 16-bit image without issues on a ‘vanilla’ Fiji install. In this case, I have only clicked on soma and end-points:
At this point you could try the following:
In Fiji, run Edit>Options>Reset… this will wipe all of IJ’s preferences which are shared across Fiji instances…
If the problem persists, run the following as a python script in the script editor After starting opening and loading your problematic image in SNT. You can use SNT’s command Scripts>New… to do so. The script will only work while SNT is open:
This will display the image exactly as snt cached it. When I ran it I got, unsurprisingly, an exact copy of the original image.