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Re: [Seg3D] Question about dilate erode element type


Chronological Thread 
  • From: jess <jess@sci.utah.edu>
  • To: massisenergy@tuta.io
  • Cc: Seg3d <seg3d@sci.utah.edu>, Sympa <sympa@lists.sci.utah.edu>
  • Subject: Re: [Seg3D] Question about dilate erode element type
  • Date: Mon, 6 Jun 2022 12:07:08 -0600
Hi Massisenergy, 

Seg3D Doesn’t really support other data types other than the structured, hexahedral-voxel data for processing and segmenting. The isosurfaces are exported as triagle surface, but Seg3D doesn’t really have the tools to generate a smooth mesh from segmentation.   Instead, we have Cleaver (https://www.sci.utah.edu/software/cleaver.html) and SCIRun (https://www.sci.utah.edu/software/scirun.html) that may help generate a smooth mesh.  

Cleaver is a fairly powerful tool that generates tetrahedral meshes with conforming boundaries.  It takes a significant amount of RAM to run, but the meshes it generates should be high quality for computation.  There is an option to save out the surface meshes in addition to the volume ones.  

SCIRun is a problem solving environment that can do isosurfacing and smoothing.  Not all the meshing tools will generate meshes good enough for computation, but will look nicer.  To get an idea how to do this in SCIRun, checkout this tutorial:  https://scirun.readthedocs.io/en/latest/user_doc/BasicTutorial.html.  You may also want to checkout the FairMesh module (https://scirun.readthedocs.io/en/latest/modules/NewField/FairMesh.html). 

Another tool (not made by us) that you can check out is MeshLab (https://www.meshlab.net).  It has many smoothing and mesh editing tools. 

cheers,
Jess




On Jun 5, 2022, at 11:30 PM, massisenergy@tuta.io wrote:

Dear,

Does Seg3D 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
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