KAHIBARO
9.2. Displaying Volumes
Table of Contents
World
To display volumes in GATE you first need to understand that the visualization system always starts from the world volume. The world is the root of the geometry tree. If the world is not visible or is misconfigured, everything inside it will either be invisible or very hard to interpret.
In OpenGATE, once you have created your simulation object and added the world volume, visualization typically becomes active when you enable a visual driver and start the simulation in interactive or visualization mode. While the details of enabling visualization are covered elsewhere, for displaying the world you mainly control its visibility, color, and level of detail.
The world is usually a very large box or sphere, often filled with air or vacuum. To make inner structures easier to see, a common approach is to set the world color to a neutral shade and keep it partially or fully transparent. Transparency is especially useful because the world volume surrounds everything. If it is opaque, all internal volumes will be hidden behind it from most viewing angles.
In a typical GATE setup, you define appearance using commands or configuration that associate visual attributes with logical volumes. For the world, you might set a simple wireframe representation or a transparent surface so that it acts as a reference frame without obstructing detector or phantom volumes. It is helpful to verify that the world size and position are correct visually; if your detectors or phantoms are not appearing, sometimes they are simply outside the world or too small compared to the world scale.
When you first open the visualization window, try zooming and rotating to confirm that the world box or boundary is visible, and that the coordinate axes behave as you expect. If you see only an empty scene, check that the world has not been defined with an extremely large size that makes objects look tiny, or that the camera is not located inside an opaque region of the world. Visual inspection of the world is often the first step in diagnosing geometry problems such as misplaced volumes or incorrect units.
Always ensure the world volume is:
1) Large enough to contain all your geometry,
2) Visible but not opaque,
3) Correctly positioned so internal volumes are inside it.
Detectors
Detectors are usually the most important volumes to inspect visually, because their placement, orientation, and repetition patterns strongly affect simulation results. In GATE, detectors are often built hierarchically: a head or ring volume that contains modules, which contain blocks or crystals. Displaying these correctly helps you verify that your logical design matches the physical scanner you want to model.
For detector volumes, it is good practice to use distinctive colors for different levels of the hierarchy. For example, you might assign one color to the detector housing, another to modules, and yet another to the individual crystals. Using different colors makes it easier to see repetitions and to identify potential mistakes such as incorrect rotations, flipped arrays, or missing components.
Transparency is crucial when displaying detectors inside housings or shielding. You can set the outer casings to be semi transparent so that the inner detector crystals are visible. When working with PET or SPECT systems, display a ring or head from several angles and zoom in on a small part of the geometry. Look carefully for gaps between crystals, overlapping crystals, or asymmetries that should not be present. Repeated volumes are particularly prone to misplacement if you mix up angles or distances.
You should also look at detector identifiers indirectly through visualization. While visualization does not show IDs directly, you can often verify that the numbering logic is consistent by building a simple color pattern or by selectively toggling visibility of particular subvolumes in the hierarchy. In a PET ring, for example, you can confirm that modules are evenly spaced around the ring and that there are no unexpected rotations that would cause misalignment with the source or phantom.
Finally, comparing the displayed detector geometry to design drawings or manufacturer specifications is an important validation step. Check crystal size, spacing, ring diameter, axial length, and orientation relative to the world axes. Visual discrepancies at this stage can prevent long and incorrect simulations later.
Always visually confirm detector:
1) Position and orientation,
2) Repetition patterns and symmetries,
3) Internal structure such as crystal arrays.
Sources
Displaying sources is mainly about confirming where particles originate and in which region of space emission occurs. In GATE, sources can be points, simple shapes such as boxes or spheres, or complex volume sources attached to existing geometries. Visualization helps you verify that the source is correctly placed inside, on, or outside a detector or phantom.
For a point source, visualization often shows a small marker or tiny volume at the source position. You should zoom in closely to ensure that this marker is exactly where you expect, such as at the center of a phantom or at a defined offset from a detector surface. If you see a point source seemingly floating at an unexpected location, check the coordinate system and units you used when defining its position.
For extended sources, such as box or spherical sources, the source region can be displayed as a volume with a distinctive color, usually semi transparent so that surrounding geometry remains visible. This helps you judge whether the emission region overlaps correctly with tissues, detector fields of view, or collimator apertures. In nuclear medicine simulations, a uniform sphere source inside a phantom is often used, and visualization immediately reveals if it is partially outside the phantom or not centered as intended.
When a source is defined as a volume source that reuses an existing geometry object, visualization becomes even more important. You need to confirm that the geometric volume you intended to use is indeed the one associated with the source, especially in complex setups with many similarly named volumes. If the source is attached to the wrong object, particle emission will occur in an unintended region, which can be hard to detect from output alone.
Source direction and angular distributions are not directly visible as shapes, but with track visualization enabled you can display a sample of particle trajectories to get an intuitive picture of emission patterns. For example, for a collimated beam you should see tracks that are approximately parallel. For an isotropic point source you should see tracks radiating in all directions. Using a small number of events with track visualization is a quick way to visually validate both source position and direction.
Always use visualization to check that:
1) Source position is correct in the chosen coordinate system,
2) Extended source shapes lie entirely within intended regions,
3) Directional or collimated sources emit in the expected directions.
Phantoms
Phantoms represent the objects that radiation interacts with, such as water phantoms, simple blocks, or full anatomical models. Displaying phantoms correctly is essential for both imaging and dosimetry simulations. Visualization lets you verify external dimensions, placement relative to detectors, and in the case of voxelized phantoms, basic structure and orientation.
Simple phantoms, such as water boxes or cylinders, are displayed as regular volumes. You typically choose colors that differentiate them from detector materials. When placing a phantom between a source and a detector, check in 3D that the beam or emitted particles must indeed pass through the phantom. Misaligned phantoms are a common cause of unexpected transmission or dose patterns.
In more complex setups, you may have several phantoms, for example an outer body phantom and inner organ phantoms. Giving each a distinct color and adjusting transparency lets you see internal structures clearly. Viewing cross sections by rotating and zooming helps to detect overlaps or gaps between phantoms that might not be physically realistic. You should also ensure that phantoms are entirely inside the world volume and not intersecting detector housing in ways that are not intended.
For voxelized phantoms built from medical images, visualization is particularly valuable, even if only a simplified representation is shown. You can check the overall shape, confirm that the patient lies in the expected orientation relative to the scanner, and verify that the head, thorax, or other regions appear where they should along the axes. This helps detect common coordinate mistakes such as flipped axes or mirrored images.
Another helpful practice is to compare phantom dimensions and positions with reference measurements or clinical setups. For example, in a water phantom simulation you might compare the size and location relative to the beam source to typical experimental arrangements. Visual alignment of isocenter, beams, and phantom center often reveals whether your geometry reflects the intended clinical or experimental configuration.
Always inspect phantoms visually to confirm:
1) Correct size and shape,
2) Proper placement between sources and detectors,
3) Reasonable alignment with real or planned experimental setups.
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