1.4. GATE Simulation Workflow

Table of Contents

Geometry

A GATE simulation always starts from the geometry, which describes every physical object in your virtual experiment or scanner. At the top level there is a world volume that contains everything else. Inside the world you place volumes that represent detector crystals, collimators, shielding, phantoms, patients, and any support structures that matter for particle transport.

In practice, you define geometry by creating volumes with specific shapes, sizes, positions, and orientations, then assigning them parent volumes. The geometry step comes first because all later parts of the simulation, such as sources and actors, must refer to specific volumes by name. During this phase you are not yet concerned with physics or data recording, only with where objects are and how they are shaped.

For most medical physics applications, the geometry must be realistic enough that radiation interactions and attenuation match the real system. Simple geometry can be defined using basic solids like boxes, cylinders, and spheres. More complex scanners can be built by repeating modules or using voxelized geometries, which you will encounter in later chapters.

Materials

Once the geometry is defined, each volume must be given a material, such as air, water, bone, or a scintillator. The material determines how particles interact in that volume, for example how likely they are to scatter or be absorbed, and how much energy they deposit per unit path length.

In the workflow, assigning materials comes immediately after defining the geometric shapes. You can use predefined materials from the Geant4 databases or define custom materials if needed. It is essential that materials match the intended physical objects. A detector crystal set to air, for instance, would essentially not detect anything because gamma rays would mostly pass through without interacting.

Materials also control quantities like density and elemental composition, which influence dose calculations and image quality. Correct material assignment is therefore a key step in any accurate simulation.

Sources

With geometry and materials in place, the next step is to define the sources of particles. In GATE, a source describes which particles are emitted, where they are emitted, in which direction, with what energy distribution, and with what activity or particle rate.

You typically attach sources to a particular volume, such as a patient phantom, a point in space, or a part of a scanner. Even when a source is not tied to a specific object, you must still specify its position relative to the world geometry, which is why sources come after geometry in the workflow.

Sources can be simple monoenergetic beams or complex radioactive sources with full decay chains. Their configuration strongly influences what parts of your geometry are irradiated and how many interactions occur. When planning a simulation, you often decide early what clinical or experimental situation you want to reproduce, then translate that into one or more GATE sources at this stage.

Physics

Physics configuration tells GATE which physical processes to simulate for the particles emitted by your sources. This is done by selecting a physics list and sometimes adjusting options such as hadronic processes or low energy electromagnetic models.

Although Geant4 contains many detailed physics models, GATE provides presets designed for medical applications. The physics step in the workflow is where you choose an appropriate set of interactions for your scenario, for example electromagnetic physics for imaging or a combination of electromagnetic and hadronic physics for proton therapy.

Along with the physics list, you also specify transport parameters like production cuts and step limits, which determine how finely particles are tracked. Physics settings come after sources because you need to know which particle types and energies will be present, but before you define data recording, since actors depend on which interactions are simulated.

In GATE, the physics list and transport parameters control which interactions are simulated and how detailed the tracking is. Incorrect physics settings can lead to physically wrong results even if the geometry and sources are correct.

Actors

Actors are tools that record information during the simulation run. Each actor is attached to a volume or the whole simulation and is responsible for computing or collecting a specific type of data, such as statistics, energy deposition, dose, or phase space.

In the workflow, you configure actors after geometry, materials, sources, and physics, because they must know what to observe and where. For example, a dose actor is attached to a phantom volume, while a statistics actor is global. Actors do not change particle transport; they simply watch and record what happens.

You can attach multiple actors to the same volume or to different volumes to obtain various outputs from a single simulation. Choosing the right actors is part of the experimental design, since they determine what quantities you will later analyze.

Digitizers

Digitizers convert physical interactions inside detectors into simulated electronic signals. While actors can record raw hits, digitizers process these hits to produce detector-level data, such as singles and coincidences in PET, that resemble what a real acquisition system would output.

Digitization is configured after actors because it operates on recorded interaction information, usually hits produced by specific actors. In this step of the workflow you define a digitizer chain that can include energy summation, detector channel identification, energy and time blurring, thresholds, and coincidence sorting.

Digitizers are especially important for imaging simulations where you want to reproduce realistic system performance, including energy resolution, timing resolution, and counting statistics. They bridge the gap between ideal physics interactions and the imperfect signals measured by actual hardware.

Simulation

Once geometry, materials, sources, physics, actors, and digitizers are set up, you are ready to run the simulation. This stage is where GATE executes the Monte Carlo transport. Particles are generated according to your source definitions, interact with the materials according to the selected physics, and all relevant information is recorded by actors and processed by digitizers.

You control the simulation run by specifying parameters such as the number of events, activity and duration, and the number of threads used. During execution, GATE writes information to the terminal showing progress, event counts, and sometimes basic statistics. At this point, you generally do not modify the configuration; instead, you monitor the run and ensure it behaves as expected.

If problems appear at this stage, such as no events being generated, empty output, or extremely slow performance, they usually indicate issues in earlier workflow steps, like an incorrectly defined source or overly complex geometry.

Output

After the simulation finishes, GATE writes output files created by your actors and digitizers. These outputs can include ROOT files with event data, image files with dose or activity distributions, and text or binary tables for other recorded quantities.

The type and structure of the output are determined entirely by what you configured in the actors and digitizer chain. For example, a dose actor will produce a voxelized dose image, while a singles digitizer will write a ROOT tree with per-event detector information. Output files are usually organized by volume or by actor, and are stored in directories that you specify in the script.

At this point the Monte Carlo transport is complete; the remaining work consists of reading, inspecting, and processing these files with dedicated analysis tools.

Analysis

Analysis is the final stage of the GATE simulation workflow, where you interpret the output to answer your scientific or engineering question. This step is not performed inside GATE itself, but with external tools such as ROOT, Python with NumPy and Pandas, or specialized medical imaging software.

Typical analysis tasks include computing energy spectra, dose distributions, depth-dose curves, coincidence count rates, image quality metrics, or detector performance figures. You may also compare simulation results with measurements or analytical models. Often, the analysis reveals that you must refine earlier workflow steps, for example adjusting the geometry, materials, physics, or digitizer configuration, and then rerun the simulation.

In practice, the workflow is iterative. You move forward from geometry to analysis, then use what you learn during analysis to improve the setup. Understanding this sequence and the role of each stage will help you structure your GATE scripts efficiently and avoid common mistakes.