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ShapeWorks Studio Groom Module

The Groom module provides options to preprocess/groom the input data. Options differ for binary segmentations and meshes. You also have the option of skipping grooming if your data is already prepped.

ShapeWorks Studio Groom Module

Image Grooming Parameters

Parameter Description
Isolate Isolate the largest object in a segmentation. This removes extraneous noise voxels that would result in disjoint objects.
Fill Holes Fill small holes in segmentation
Crop Crop image down to ROI of segmentation
Pad Pad image with zeroes by a given number of voxels. Typically combined with cropping
Antialias Perform anti-aliasing to reduce segmentation stairstep effect
Resample Resample image spacing either to isotropic (recommended) or any given spacing
Distance Transform Create a distance transform for image based optimization
Blur Perform smoothing on the distance transform using a gaussian blur
Convert to Mesh Optionally convert to mesh at the end of Image Grooming. This enables the Mesh Grooming pipeline and will run the optimization on meshes

Mesh Grooming Parameters

Parameter Description
Fill Holes Fill small holes in the mesh
Smooth Perform either Laplacian or Windowed Sinc smoothing
Laplacian Smoothing Laplacian smoothing option with specified iterations and relaxation factor. In general, it is recommended to use smaller relaxation factors and more iterations rather than larger relaxation and fewer iterations
Windowed Sinc Smoothing Windowed Sinc smoothing with specified iterations and passband (typically between 0 and 2). Lower passpand values produce more smoothing.
Remesh Enabled remeshing using ACVD library
Remesh Percent Specify target vertices as a percentage of existing vertices
Remesh Vertices Specify target vertices directly
Remesh Adaptivity Curvature adaptivity of remeshing (0 = uniform, 2.0 most adaptive). This allocates more triangles/vertices to areas of higher curvature

Alignment Parameters

Parameter Description
Reflect Option to reflect some shapes over a given axis if a given column matches a given value (e.g. reflect 'side' over 'Y' if 'left')
Alignment Option to align with centering (center of mass), iterative closest point (translation and rotation), or landmarks (best fit, when specified)