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# 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.

Demonstration

- Bounding Box demonstration

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 X, Y, Z, min fields to set the starting point of the dataset, or the X, Y, center fields to define its center, which automatically recalculates minimal coordinates.

Maximal coordinates (X, Y, Z max) can be set to adjust voxel sizes, and a Stage rotation bias, degrees field accounts for acquisition biases, such as the 45-degree tilt in Gatan 3View systems.

Click the Apply button to update the dataset’s bounding box, or use Cancel 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

- X, Y, Z, min define the minimal coordinates of the bounding box (e.g., the lower-left-front corner in 3D space).
- X, Y, center specify the central coordinates of the dataset; automatically recalculates X, min and Y, min based on dataset dimensions.
- X, Y, Z max set the maximal coordinates; when used with minimal coordinates, recalculates voxel sizes to match the new bounding box dimensions.
- Stage rotation bias, degrees adjust for stage rotation bias in degrees (e.g., enter 45 for Gatan 3View’s default tilt).
- Import from Clipboard 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 Import from Clipboard to set voxel size for the current dataset.

    ScaleX = 0.015
    ScaleY = 0.015
    ScaleZ = 0.05

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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