Bounding Box
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Description
The Bounding Box defines the position of the dataset in 3D space, which is crucial for accurate positioning in visualization software like Amira or for aligning multiple datasets.
Adjust the bounding box by specifying its minimal or central coordinates, or import settings from the clipboard. Current coordinates are displayed under the Current Bounding Box text in the dialog.
Use the
fields to set the starting point of the dataset, or the fields to define its center, which automatically recalculates minimal coordinates.Maximal coordinates (
) can be set to adjust voxel sizes, and a field accounts for acquisition biases, such as the 45-degree tilt in Gatan 3View systems.Click the
button to update the dataset’s bounding box, or use to close the dialog without changes.Bounding Box Note
For 3D images, the bounding box is calculated as the smallest box containing all voxel centers, not all voxels. It’s defined by voxel centers, meaning 1/2 voxel is subtracted on both sides, resulting in a box 1 voxel smaller in all three directions.
Widgets and parameters
- define the minimal coordinates of the bounding box (e.g., the lower-left-front corner in 3D space).
- specify the central coordinates of the dataset; automatically recalculates and based on dataset dimensions.
- set the maximal coordinates; when used with minimal coordinates, recalculates voxel sizes to match the new bounding box dimensions.
- adjust for stage rotation bias in degrees (e.g., enter 45 for Gatan 3View’s default tilt).
- parse text from the system clipboard to set bounding box parameters (see below for syntax).
Import from clipboard settings
Syntax: [ParameterName] = [ParameterValue]
to extract parameters.
Parameter Name | Description |
---|---|
ScaleX | Physical size of pixels in X (e.g., micrometers per pixel) |
ScaleY | Physical size of pixels in Y (e.g., micrometers per pixel) |
ScaleZ | Physical size of pixels in Z (e.g., micrometers per pixel) |
xPos | Central position of the dataset in the X plane |
yPos | Central position of the dataset in the Y plane |
Z Position | Minimal Z coordinate |
Rotation | Rotation bias (MIB adds 45 degrees for Gatan 3View compatibility) |
Example 1
Copy the following text into the system clipboard and press
to set voxel size for the current dataset.Example 2
Magnification = 897x
Voltage = 2500 V
ScaleX( µm) = 0.0150039
ScaleY( µm) = 0.0150039
xPos (um) = -103.759
yPos (um) = -535.899
ScaleZ (µm) = 0.05
Z Position (um) = 58.9802
Dwell time = 8 ms
Spot Size = 3000
Pressure (Torr) = 0.0865544
Rotation = 0
Working Distance (mm) = 5.64201
Width x Height = 7000 x 7000
Acquisition Date = 24/03/2025
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