Morphology Operations

The Morphology Operations tool applies mathematical morphology operations to volume or mask objects. These operations modify object shapes based on a structuring element and are fundamental for shape analysis, noise removal, and object separation.

Accessing the Tool

1. Navigate to the Image tab in the ribbon.
2. Click Morphology Operations in the Operations section.

Parameters

Target Objects

Select objects to process. The list covers volumes and masks alike, because morphology works on either:

• Active volume object, Selected volume object(s), Visible volume object(s), All volume objects
• Active mask object, Selected mask object(s), Visible mask object(s), All mask objects

Operation Type

Operation	Description
Erode	Shrinks objects by removing pixels from boundaries
Dilate	Expands objects by adding pixels to boundaries
Open	Erosion followed by dilation; removes small protrusions
Close	Dilation followed by erosion; fills small holes and gaps

Structuring Element

Define the kernel (structuring element) size for the operation:

The group is titled Structuring element ball radius, and the element is a ball with the radii you give it:

Parameter	Range	Default	Description
X (pixels)	1 to 50	7	Radius of the neighbourhood along X
Y (pixels)	1 to 50	7	Radius of the neighbourhood along Y
Z (pixels)	1 to 50	1	Radius of the neighbourhood along Z
Isotropic			Ties the three radii together, so changing one changes all three

note

The default Z radius of 1 makes the operation almost in-plane, which suits data whose slice spacing is much larger than its in-plane spacing. For an isotropic volume, tick Isotropic so the structuring element is a true sphere and the result is direction independent.

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Operation Details

Erode

Erosion removes pixels at object boundaries:

• Objects shrink inward
• Small objects may disappear entirely
• Connections between objects may break
• Useful for separating touching objects

Effect: A pixel is eroded (set to background) if any part of the structuring element extends outside the object.

Dilate

Dilation adds pixels at object boundaries:

• Objects grow outward
• Small gaps between objects may close
• Useful for filling small holes
• Can connect nearby objects

Effect: A pixel is dilated (set to foreground) if any part of the structuring element touches the object.

Open (Erosion → Dilation)

Opening removes small bright features and thin connections:

• Smooths object contours
• Removes small protrusions (spurs)
• Breaks thin bridges between objects
• Preserves overall object shape

Use case: Cleaning up noisy segmentations by removing small artifacts.

Close (Dilation → Erosion)

Closing fills small dark features and gaps:

• Smooths object contours
• Fills small holes
• Connects nearby objects
• Bridges narrow breaks

Use case: Completing segmentations by filling internal holes.

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Workflow

1. Open the Morphology Operations tool.
2. Select target objects from the dropdown.
3. Choose the operation type (Erode, Dilate, Open, Close).
4. Set the structuring element radii.
5. Enable Isotropic for uniform processing in all directions.
6. Click Apply to perform the operation.

Use Cases

Separating Touching Objects

When segmented objects touch and need to be separated:

1. Apply Erode with appropriate radius.
2. Objects shrink and separate.
3. Use connected component analysis to label individual objects.
4. Optionally Dilate to restore approximate original size.

Filling Holes in Segmentation

When segmentation contains unwanted internal holes:

1. Apply Close with radius larger than the holes.
2. Holes are filled while outer boundaries remain similar.

Removing Small Artifacts

When segmentation contains small noise spots:

1. Apply Open with radius larger than the artifacts.
2. Small isolated regions disappear.
3. Larger objects remain with smoothed boundaries.

Smoothing Jagged Boundaries

For cleaner segmentation edges:

1. Apply Close followed by Open, or vice versa.
2. Jagged edges become smoother.
3. Adjust radii to control smoothing strength.

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Parameter Guidelines

Scenario	Operation	Suggested Radius
Remove small spots	Open	2–5 pixels
Fill small holes	Close	2–5 pixels
Separate objects	Erode	Depends on gap needed
Smooth boundaries	Open + Close	1–3 pixels

tip

Use smaller radii for subtle adjustments and larger radii for more aggressive modifications. Preview results before applying to large datasets.

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2D vs 3D Processing

The structuring element operates in 3D when Z radius > 0:

Z Radius	Processing Mode
1 (or more)	Full 3D morphology
Very small	Approximately slice-by-slice

info

For consistent 3D objects, use similar radii in all directions (isotropic). For slice-based data, you may want smaller Z radius.

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Scripting

Morphological operations are available via the Python scripting API.

import ScriptingApi as api

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

# Erode with ball radius [7, 7, 1] pixels
volume_operations.morphological_operation(
    ["Volume1"],
    api.MorphologicalOperation.Erode,
    [7, 7, 1]  # radius [x, y, z]
)

# Dilate
volume_operations.morphological_operation(["Volume1"], api.MorphologicalOperation.Dilate, [5, 5, 5])

# Open
volume_operations.morphological_operation(["Volume1"], api.MorphologicalOperation.Open, [3, 3, 3])

# Close
volume_operations.morphological_operation(["Volume1"], api.MorphologicalOperation.Close, [3, 3, 3])

See the VolumeOperations API Reference for details.

warning

Morphological operations modify data directly. Excessive erosion may remove important structures; excessive dilation may merge separate objects.