First of all it’s good to be able to build a more detailed understanding of the difference between the smoothing under the Show 3D button and the joint smoothing algorithm applied under the Smoothing effect. I suppose that implicitly I had an idea that the former smooths the surface representing the boundary of the segmented voxels (which you call the mesh), while the latter smooths the segment by adding or removing voxels (which you call the labelmap). Thank-you for additional clarification.
For the record (as some of you would already have realised), the above screenshots were taken without any mesh smoothing. I presented the geometry in this way so that the source of the artefacts would be more immediately obvious.
If I apply mesh smoothing to the above two segments, with Smoothing factor equal to 0.5, then the results are as below.
So indeed the gap is preserved by smoothing the mesh, rather than the labelmap.
However, aside from the bridging artefacts, I prefer the smoothing obtained by smoothing the labelmap first and then smoothing the mesh.
While this is a logical suggestion, there may be a couple of potential issues.
Firstly, I have already increased the resolution by a minimum of fourfold in each orthogonal direction by isotropic cropping in the Crop Volume module.
I’m reluctant to increase the resolution of the cropped volume much more than that, because it may create massive 3D rasters that would be (I think) slower to process. Especially so if I go through slice-by-slice to manually amend the initial results (obtained by thresholding or grow-from-seeds, say).
I’m also not sure that it’d be suitable to increase the resolution of the labelmap only.
Presumably this would be done through the Segmentation geometry dialogue, per the screenshot below. [DIGRESSION: we’ve had a little discussion of this topic before. Incidentally, it seems a little inconsistent that in this dialogue a factor >1 is needed to increase resolution, whereas in the Crop Volume module a factor <1 is needed to increase resolution.]
The additional issue I anticipate is that then the smoothing would end up being highly localised (or ‘small scale’). Suppose I have two 5-millimetre objects separated by a small gap (say 0.2 mm). If I use a resolution of, say, 0.05 mm, then most likely the gap will be preserved, but I may end up with smooth medium-sized artefacts (0.5–1 mm bumps, say) on the larger objects that I’m unable to smooth away. Or, to put it another way, I imagine that the smoothing kernel (or some equivalent) will be smaller if the resolution is increased.
In the end I think the results look best if I manually erase the erroneous voxels, as below.
—DIV