Musiré

Multimodal simulation and reconstruction framework for the radiological imaging sciences

Musiré is a software-based workflow for managing the execution of simulation and image reconstruction for SPECT, PET, CBCT, MRI, BLI and FMI packages in single and multimodal biomedical imaging applications [1].

The workflow is composed of a Bash script, the purpose of which is to provide an interface to the user, and to organize data flow between dedicated programs for simulation and reconstruction.

The currently incorporated simulation programs comprise: 

• GATE for Monte Carlo simulation of SPECT, PET and CBCT, 
• SpinScenario for simulating MRI, and 
• Lipros for Monte Carlo simulation of BLI and FMI

Currently incorporated image reconstruction programs include 

• CASToR for SPECT and PET
• RTK for CBCT.

MetaImage (mhd) standard is used for voxelized phantom and image data format. Meshlab project (mlp) containers incorporating polygon meshes and point clouds defined by the Stanford triangle format (ply) are employed to represent anatomical structures for optical simulation, and to represent tumour cell inserts. A number of auxiliary programs have been developed for data transformation and adaptive parameter assignment. The software workflow uses fully automatic distribution to, and consolidation from, any number of Linux workstations and CPU cores.

Example data are presented using:

• the Mida head phantom for clinical SPECT, PET and MRI systems and
• the Digimouse phantom for preclinical X-ray, PET and BLI systems

The presented method unifies and simplifies multimodal simulation setup and image reconstruction management and might be of value for synergistic image research.

GitHub Page

Installation Guide

Usage Guide

Reference

[1] Peter, J. (2021) Musiré: multimodal simulation and reconstruction framework for the radiological imaging sciences Phil Trans Royal Society A, Vol 379, Issue “Synergistic Tomographic Image Reconstruction: Part 2”, DOI: 10.1098/rsta.2020.0190

Disclaimer & Copyright

Musiré is provided as an open-source project and will be continuously developed. Please make sure that your usage of this code is in compliance with the Apache License 2.0. The purpose of this project is only for academic research excluding any clinical study. To make it better, you are very welcome to contribute in many ways such as to add simulation and reconstruction parameters, to improve the existing script and to add new features to it, to provide interfaces to software that might be incorporated from Musiré, or to find and correct software mistakes.

Copyright © German Cancer Research Center (DKFZ), Division of Medical Physics in Radiology.