The 3D tracing algorithms use the data from the image displayed in the 3D window. For this reason, it is important to make adjustments prior to tracing if the image doesn't display as expected (too dark, not clear enough, etc.) and/or if you're only interested in one channel in a multichannel image.
To make adjustments, use the gamma, white point, and black point settings in the Image panel. Adjustments are applied to all the displayed data.
To make adjustments on a per channel basis, use Image Adjustment available from the classic window. See Tracing from a multichannel image (3D)