Shrink

The Shrink tool reduces the image extent to match the bounding box of objects in the project. Unlike cropping, which uses a user-defined region, shrinking automatically calculates the minimal bounds needed to contain all relevant data.

Accessing the Tool

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

How It Works

The Shrink operation:

1. Analyzes the spatial extent of objects in the project.
2. Calculates the minimal bounding box that contains all object geometry.
3. Resizes the volume and mask data to match these bounds.
4. The output size exactly matches the calculated bounds.

Difference from Crop

Feature	Crop	Shrink
Bounds	User-defined	Automatically calculated
Scope	Fixed region	Adapts to object boundaries
Use case	Manual region selection	Automatic size optimization

Parameters

Target Objects

Select which objects to process:

• Active mask
• Selected masks
• Visible masks
• All masks
• Active surface
• Selected surfaces
• Visible surfaces
• All surfaces
• Visible masks and visible surfaces
• All masks and all surfaces

Padding

Optional padding around the calculated bounds:

Mode	Description
Uniform padding	Add same padding to all sides (X-, Y-, Z-, X+, Y+, Z+)
Non-uniform padding	Specify individual padding for each direction

Workflow

1. Ensure objects (surfaces, masks, or other geometry) are present in the project.
2. Open the Shrink tool from the Image tab.
3. Select target objects for boundary calculation from the dropdown.
4. Optionally enable Uniform padding and specify padding value (0-1023 pixels).
5. For non-uniform padding, disable uniform padding and set individual values:
   • X- (left), Y- (bottom), Z- (front)
   • X+ (right), Y+ (top), Z+ (back)
6. Click Apply to shrink the selected objects to their calculated bounds plus padding.

Use Cases

Optimizing Data After Surface Generation

After creating surface meshes from segmented data:

1. The original volume may contain large empty regions.
2. Use Shrink to reduce the volume to the extent of the surfaces.
3. Reduces memory usage and speeds up visualization.

Preparing Data for Export

Before exporting data for external processing:

1. Shrink to remove unnecessary padding.
2. Results in smaller file sizes.
3. Faster data transfer and processing.

Affected Objects

The Shrink operation affects:

• All volume objects
• All mask objects

All datasets are shrunk to the same bounds to maintain spatial alignment.

warning

Shrinking is a destructive operation. Data outside the calculated bounds is permanently removed. Save your project before shrinking if you need to preserve the original extent.

Scripting

This operation is available via the Python scripting API using shrink().

import ScriptingApi as api

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

# Shrink to specified bounds [xMin, xMax, yMin, yMax, zMin, zMax] in millimeters
volume_operations.shrink(["Volume1"], [-25.0, 25.0, -30.0, 30.0, 0.0, 80.0])

See the VolumeOperations API Reference for details.

info

When shrinking based on surface objects, the bounds are calculated from the surface geometry. If surfaces extend beyond the current volume extent, the operation adjusts accordingly.