Dilation erosion element type

[massisenergy]

Dear,

Does 3DSlicer offer any more element types (sphere, circle, rectangle etc.) than squared pixels?

For example, I have a tomography image which is high resolution (very small pixel size). That, upon surface-export, results in a jagged isosurface with very large number of triangles which I do not need.

If I could use a sphere or ball as my dilation-erosion element of chosen size, I could get a lot smoother, non-pixelated (and less number of triangle) surface for my use case.

Any information / advice on this will be highly appreciated.

With regards,
massisenergy

[mau_igna_06 (Mauro I. Dominguez)]

You can get reducing the numer of triangles by using decimation on your mesh… If I were you I would set it to 6% and see how it gets

[massisenergy]

Hello,

Thanks for your suggestion. Unfortunately ‘Decimate’ doesn’t work for my use case. It couldn’t remove the jagged edges, rather resulted in bad quality triangles.

Then I tried using the Surface Models > Advanced > Smoothing. After playing with the parameters (Iterations: 100, Relaxation: 0.1) , I could reduce the jagging a lot but not without a ~15% decrease in the overall volume!

Any other ideas, folks?

[mau_igna_06 (Mauro I. Dominguez)]

Maybe you can try some kind of lapalacian smoothing filter for polydata and then decimate
Maybw try with rhe taubin one.

Hopw it helps

[pieper (Steve Pieper (Isomics, Inc.))]

It looks like your input data was pixelated (binarized) before the original surface was generated. Starting with an original continuous tone scan would be the normal way to generate a smooth isosurface.

[massisenergy]

@mau_igna_06 Okay. Reducing the total number of triangles isn’t hard anymore, Blender (v 3.1.2) serves the purpose quite well. I tried with the Taubin option as well, that also removes volume while smoothing!

@pieper exactly. I got a binary pixelated tomography data and I have make smooth surface out of it. You’re absolutely in the right direction:

@pieper

Starting with an original continuous tone scan would be the normal way to generate a smooth isosurface.

I realise that even if Slicer offers sphere type (which is not available at the moment I guess?) dilation or erosion elements, simply working with those on square pixelated tomography data would inevitably result in the loss of some volume .

So my question now changes into – Is it possible to get smooth surface out of binary pixelated data (negligible loss of volume)?

[pieper (Steve Pieper (Isomics, Inc.))]

If the mesh-based smoothing is failing (which make some sense given that the data is basically aliased) then converting the mesh to an image, smoothing in image space, and re-isosurfacing may work better. You will have options about kernel size, weights, and thresholds so you can see what works best for that data.

[massisenergy]

Thanks all. For now, I used the Blender provided smoothing tools, but generating the surface without any “voxelized segmentation” would be best if smoothing induced volume loss is unacceptable!