Smooth Mask

The Smooth Mask tool applies smoothing filters to mask objects to improve boundary quality and reduce noise artifacts. Smoothing helps create cleaner masks for visualization and downstream processing such as surface generation.

Accessing the Tool

1. Navigate to the Segmentation tab in the ribbon.
2. Click Smooth Mask in the Operations section.

Smoothing Filters

Discrete gaussian

Applies a Gaussian blur using discrete kernel approximation:

Parameter	Description
Sigma X (pixels)	Standard deviation in X direction (default: 1.0, decimals: 1).
Sigma Y (pixels)	Standard deviation in Y direction (default: 1.0, decimals: 1).
Sigma Z (pixels)	Standard deviation in Z direction (default: 1.0, decimals: 1).
Isotropic	Use the same sigma for all directions.

Larger sigma values produce more smoothing but may erode fine details.

Recursive gaussian

Efficient Gaussian smoothing using recursive implementation:

Parameter	Description
Sigma X (pixels)	Standard deviation in X direction (default: 1.0, decimals: 1).
Sigma Y (pixels)	Standard deviation in Y direction (default: 1.0, decimals: 1).
Sigma Z (pixels)	Standard deviation in Z direction (default: 1.0, decimals: 1).
Isotropic	Use the same sigma for all directions.

Faster for large sigma values compared to discrete Gaussian.

Mean

Replaces each voxel with the average of its neighborhood:

Parameter	Description
Radius X (pixels)	Neighborhood radius in X direction (default: 1, max: 99).
Radius Y (pixels)	Neighborhood radius in Y direction (default: 1, max: 99).
Radius Z (pixels)	Neighborhood radius in Z direction (default: 1, max: 99).
Isotropic	Use the same radius for all directions.

Median

Replaces each voxel with the median of its neighborhood:

Parameter	Description
Radius X (pixels)	Neighborhood radius in X direction (default: 1).
Radius Y (pixels)	Neighborhood radius in Y direction (default: 1).
Radius Z (pixels)	Neighborhood radius in Z direction (default: 1).
Isotropic	Use the same radius for all directions.

Effective for removing salt-and-pepper noise while preserving edges.

Parameters

Target Objects

Option	Description
Active mask	Apply to the currently active mask only.
Selected masks	Apply to all selected masks.
All masks	Apply to every mask in the project.
Visible masks	Apply to all visible masks.

Workflow

1. Open the Smooth Mask tool from the Segmentation tab.
2. Select the Target Objects to smooth.
3. Choose a Smoothing Filter type.
4. Configure the filter parameters (sigma, radius, etc.).
5. Click Apply to execute the smoothing operation.

Filter Selection Guide

Filter	Best For	Edge Preservation
Discrete Gaussian	General smoothing	Low
Recursive Gaussian	Large-scale smoothing	Low
Mean	Uniform noise reduction	Low
Median	Salt-and-pepper noise	High

tip

Use median filtering when you need to remove isolated noisy voxels while maintaining edge sharpness. Use Gaussian filters for overall boundary smoothing.

Technical Notes

Smoothing operations on binary masks produce fractional values at boundaries. After smoothing, you may need to:

1. Binarize the mask to restore strict on/off values.
2. Accept partial volume representation for more accurate boundary modeling.

Use Cases

• Pre-Surface Generation: Smooth masks before converting to surface meshes.
• Noise Reduction: Remove segmentation artifacts and isolated voxels.
• Boundary Refinement: Create smoother object boundaries.

See Also

• Binarize — Convert to binary after smoothing.
• Refine Mask — Automatic mask cleanup.
• Morphology Operations — Dilate/erode operations.
• Segmentation Tab Overview — Overview of all segmentation tools.