Padding

The Pad and Surface-Guided Pad tools add voxels around the borders of volume and mask data, extending the image extent. Padding is useful for ensuring sufficient space around objects for processing operations or to accommodate geometry that extends to the image boundaries.

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Pad

The standard Pad tool adds a specified number of voxels to each side of the image.

Accessing the Tool

1. Navigate to the Image tab in the ribbon.
2. Click Pad in the Transform section.

Parameters

Uniform Padding

Enable Uniform padding to add the same number of voxels on all sides:

Parameter	Description
Pixels	Number of voxels to add uniformly (1–1023)

Directional Padding

Disable uniform padding to specify padding for each direction independently:

Parameter	Description
-X	Voxels to add at the lower X boundary (0-1023)
+X	Voxels to add at the upper X boundary (0-1023)
-Y	Voxels to add at the lower Y boundary (0-1023)
+Y	Voxels to add at the upper Y boundary (0-1023)
-Z	Voxels to add at the lower Z boundary (0-1023)
+Z	Voxels to add at the upper Z boundary (0-1023)

Padding Value

New voxels are initialized to zero (background intensity).

Workflow

1. Open the Pad tool from the Image tab.
2. Choose between Uniform or Directional padding.
3. Enter the desired padding values in pixels.
4. Click Apply to add padding.

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Surface-Guided Pad

The Surface-Guided Pad tool automatically calculates the padding required to ensure surface objects remain within the volume bounds.

Accessing the Tool

1. Navigate to the Image tab in the ribbon.
2. Click Surface-Guided Pad in the Transform section.

How It Works

1. The tool analyzes the extents of selected surface objects.
2. It calculates how much each surface extends beyond the current volume bounds.
3. Padding is automatically applied to contain all surfaces.

Parameters

Parameter	Description
Target volume	The volume to which padding will be applied
Surface objects	Surfaces used to calculate required padding

Use Case

When surface meshes extend beyond the volume boundaries (e.g., after smoothing or modification):

1. Operations requiring the surface to be within the volume may fail.
2. Surface-Guided Pad automatically resolves this issue.
3. The volume is expanded minimally to contain all surfaces.

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When to Use Padding

Before Morphological Operations

Erosion and dilation operations may produce unexpected results at image boundaries. Add padding to:

• Ensure consistent behavior at edges
• Prevent boundary artifacts

After Surface Modifications

If surface processing (smoothing, subdivision) causes geometry to extend beyond volume bounds:

• Use Surface-Guided Pad to automatically expand the volume
• Maintains proper spatial relationship between surfaces and volumes

For Simulation Boundaries

Finite element or CFD simulations may require buffer zones:

• Add padding to create space for boundary conditions
• Ensure simulation domains don't clip important geometry

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Affected Objects

Padding affects:

• All volume objects
• All mask objects

All datasets are padded equally to maintain spatial alignment.

info

Padding increases memory usage proportionally. A 10-pixel uniform pad on a 500×500×500 volume increases size to 520×520×520, adding approximately 13% more voxels.

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Scripting

Padding operations are available via the Python scripting API.

import ScriptingApi as api

app = api.Application()
volume_operations = app.get_volume_operations()

# Add padding (lower and upper bounds in voxels)
volume_operations.pad(
    ["Volume1"],
    [10, 10, 10],    # Lower bound padding [x, y, z]
    [10, 10, 10]     # Upper bound padding [x, y, z]
)

# Surface-guided padding
volume_operations.surface_guided_padding("Volume1", ["Surface1", "Surface2"])

See the VolumeOperations API Reference for details.

warning

Padding modifies image origin and extent metadata. Verify coordinate alignment after padding if precise positioning is required.