Resources

This page contains links to Monte-Carlo simulation programs, image viewer software, as well as to alternative reconstruction platforms proposed by other research groups.

 

Monte-Carlo simulation platforms

 

  • GATE : GATE is an advanced open-source software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), Computed Tomography (CT), Optical Imaging (Bioluminescence and Fluorescence) and Radiotherapy experiments. CASToR contains several toolkits to convert root data to CASToR format.

 

  • SIMIND : SIMIND is an open-source software allowing to describe a standard clinical SPECT camera. It can easily be modified for almost any type of calculation or measurement encountered in SPECT imaging. SIMIND has been developed by Professor Michael Ljungberg. The distribution includes the smc2castor program to convert data from SIMIND to the CASToR format.

 


Image viewer software

 

CASToR output image file format is Interfile. It is composed of a pair of files: an ASCII (text file) header containing meta-data about the image (dimensions, data type, etc..), and a binary file containing the raw image matrix flattened into an array. Although numerous software should be able to read image in interfile format, some differences in interfile keys can lead to reading errors. The following software can read Interfile images generated by CASToR from version 2.0 :

 

  • AMIDE : A free software for viewing, analyzing, and registering volumetric medical imaging data sets using GTK+. It is available for Windows and Unix-based systems.

 

  • ImageJ : Java-based image processing program developed at the National Institutes of Health, available on Windows and Unix-based systems. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Since CASToR v2.0, the output images can be directly read using the NucMed plugin.

 

  • VINCI : VINCI was designed for the visualization and analysis of volume data generated by medical tomographical systems with special emphasis on the needs for brain imaging with Positron Emission Tomography (PET). VINCI is highly modular, extensible, compact and runs well on a wide range of systems.

 

Alternatively, the output images can be directly read in raw format. Most image viewers and scripting languages allow to directly open the binary file (.img) as long as the user manually provides information about image matrix dimensions and data type, and possibly voxel size. Most of this information is contained in the text header file (.hdr). The binary file contains only the raw image matrix flattened into an array using C order.

 


Other reconstruction platforms and programs (non-exhaustive list)

 

  • ASTRA toolbox : MATLAB and Python toolbox of high-performance GPU primitives for 2D and 3D tomography

 

  • Gadgetron : Open source framework for medical image reconstruction, with an emphasis on MRI

 

  • NiftyRec : Software for tomographic reconstruction using MATLAB and Python interfaces and providing GPU-accelerated reconstruction tools for PET, SPECT and CT

 

  • Occiput : Computing platform for tomographic reconstruction with tools for SPECT, PET and (partly) CT based on a Python library and a web-based interface enabling the use of the reconstruction tools on the cloud

 

  • QSPECT : SPECT reconstruction package including MLEM/OSEM algorithms

 

  • RTK : ITK-based package focused on cone-beam CT reconstruction

 

  • STIR : Open Source software providing a Multi-Platform Object-Oriented framework for image reconstruction in PET and SPECT

 

  • TIGRE : MATLAB and CUDA toolbox for fast and accurate 3D tomographic reconstruction providing a wide range of iterative algorithms for Cone Beam CT geometries

 

Other alternative platforms are listed on the RTK and STIR websites.