YRT-PET documentation

Compilation

• Building YRT-PET
  • Requirements
  • Configuration and compilation
  • FAQ
• Adding plugins to YRT-PET

Usage

• Command line interface
• Python interface
• YRT-PET Configuration
  • Number of threads
  • Disabling page-locked memory (or pinned memory)
  • From Python
• Dynamic Framing
  • Python Usage
  • File Format
  • Notes

File formats

• Data formats
  • Scanner (Scanner)
  • Image format (Image)
  • YRT-PET raw data format (Array)
  • Listmode (ListmodeLUT)
  • Sparse histogram (SparseHistogram)
  • Motion information (LORMotion)
  • Histogram (Histogram3D)
• Scanner definition
  • Scanner parameters
  • Look-Up-Table
• Image
  • Image parameters
  • Image file format
  • Fourth Dimension (Time)
  • For Python users and plugin developers
• List-mode file
  • For Python users
• List-mode DOI file
• Motion information file
• Histogram3D format
  • File format
  • Array format
  • Crystals in the same ring
  • Binning for different rings
  • Dealing with multiple DOI layers
  • Histogram Dimensions
  • Example
  • Small asymmetry in the Histogram
• RAWD format
• Sparse histogram file
  • Implementation
• Image-Based PSF File Format
  • Uniform PSF Kernel
  • Spatially Variant PSF Kernel (PSF LUT)

Python

• Array
  • Overview
  • Supported Types
  • Memory management
  • Data Access
  • NumPy Interoperability
  • Boolean Array example
• Vector3D and Line3D
  • Vector3D
  • Line3D
  • Practical Example: Creating LORs for Projection
  • Notes
• Projector
  • Available Projector Types
  • Python Usage
  • Siddon vs Distance-Driven
  • Siddon-specific Methods
  • Single LOR Projection Methods (Siddon)
  • Notes
• Bin Iterator
  • Python Types
  • Available Iterators
  • For plugin developers
• OperatorProjector
  • Python Usage
  • Important methods
• ProjectionList
  • Python Usage
  • Owned vs Alias
• Owned vs Alias (For Python users and Plugin developers)
  • Examples
• OSEM
  • Basic Usage
  • Configuration
  • Output
• Constraints
  • Python Types

Other

• Frequenty asked questions
• Contributing
  • Git feature development workflow
  • Testing
  • Code standard
  • Reconstruction code basis
  • Priority functionality
  • Wish list for a full product

Current YRT-PET version:

2.0.4

Citing YRT-PET:

If you use YRT-PET in one of your projects, you can cite our journal article in IEEE Transactions on Radiation and Plasma Medical Sciences.

@article{najmaoui2025,
    title = {{YRT}-{PET}: An Open-Source {GPU}-Accelerated Image
        Reconstruction Engine for Positron Emission Tomography},
    issn = {2469-7303},
    url = {https://ieeexplore.ieee.org/document/11202639},
    doi = {10.1109/TRPMS.2025.3619872},
    journal = {{IEEE} Transactions on Radiation and Plasma Medical
        Sciences},
    pages = {1--1},
    author = {Najmaoui, Yassir and Chemli, Yanis and Toussaint, Maxime and
        Petibon, Yoann and Marty, Baptiste and Fontaine, Kathryn and
        Gallezot, Jean-Dominique and Razdevšek, Gašper and Orehar, Matic and
        Dhaynaut, Maeva and Guehl, Nicolas and Dolenec, Rok and
        Pestotnik, Rok and Johnson, Keith and Ouyang, Jinsong and
        Normandin, Marc and Tétrault, Marc-André and Lecomte, Roger and
        El Fakhri, Georges and Marin, Thibault},
    year = {2025},
    keywords={Image reconstruction;Biomedical imaging;Graphics processing
        units;Software;Positron emission tomography;Python;Engines;Software
        algorithms;Plasmas;Geometry;positron emission tomography (PET);image
        reconstruction;software;graphics processing unit (GPU);C++;Python}
}