Crop

The Crop tool removes voxels outside a defined bounding box, reducing the image extent and file size. Use cropping to focus on a region of interest and eliminate empty or irrelevant regions.

Accessing the Tool

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

Cropping Interface

When the Crop tool is activated, an interactive bounding box appears in the 3D and 2D views.

Options

Option	Description
Enable cropping	Toggle real-time preview of the cropped region
Show box	Display or hide the bounding box wireframe

Bounds

Define the crop region using pixel ranges for each axis:

Parameter	Description
Min X – Max X	Horizontal extent (left to right)
Min Y – Max Y	Vertical extent (bottom to top)
Min Z – Max Z	Depth extent (front to back)

Use the sliders or enter values directly to adjust each range.

Interactive Adjustment

• Drag box faces: Click and drag the faces of the bounding box in the 3D view to resize.
• Drag box edges: Adjust two dimensions simultaneously.
• Drag box corners: Resize all three dimensions at once.

Information Panel

The tool displays dimensional information to help you understand the cropping effect:

Field	Description
Input physical dimensions	Original volume size in millimeters
Output physical dimensions	Cropped volume size in millimeters
Input voxel dimensions	Original volume size in pixels
Output voxel dimensions	Cropped volume size in pixels
Input box dimensions	Bounding box size in millimeters
Output box dimensions	Resulting crop region size in millimeters

Workflow

1. Open the Crop tool from the Image tab.
2. Enable Show box to visualize the crop region.
3. Adjust the Min/Max sliders for X, Y, and Z to define the region of interest.
4. Review the Information panel to verify the output dimensions.
5. Click Reset to restore the original bounds if needed.
6. Click Apply to perform the crop operation.

warning

Cropping is a destructive operation that permanently removes voxel data outside the crop region. Save your project before cropping if you need to preserve the original data.

Affected Objects

Cropping affects:

• All volume objects in the project
• All mask objects in the project

Both volumes and masks are cropped to the same bounds to maintain spatial alignment.

Use Cases

Reducing File Size

Large datasets often contain significant empty or background regions. Crop to the region containing actual data to:

• Reduce memory usage
• Speed up processing operations
• Decrease project file size

Isolating Regions of Interest

Focus analysis on specific anatomical regions:

1. Navigate to the region of interest in slice views.
2. Adjust crop bounds to enclose only the target region.
3. Apply the crop.
4. Subsequent operations process only the relevant data.

Scripting

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

import ScriptingApi as api

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

# Crop bounds: [xMin, xMax, yMin, yMax, zMin, zMax] in millimeters
volume_operations.crop(["Volume1"], [-50.0, 50.0, -50.0, 50.0, 0.0, 100.0])

See the VolumeOperations API Reference for details.

info

If the specified bounds extend beyond the original image extent, only the overlapping region is retained.