One of our highlight topics is the Monte Carlo simulation of emission imaging, that is eV and keV photon propagation in heterogeneous phantoms and diverse scanner and detector geometries, all of which within a unique, easy to use multimodal framework, Musiré, that enables not only the use of 3D meshs and/or voxelized data across all involved modalities with seamless transformation and adaption between them but also, for the first time, the integration of tumor lesions as defined by (tumor) cell clouds that are the results of biological cancer simulations.

With Musiré, a software-based workflow is proposed 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. 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 as well as 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.

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