Semester Project at CERN (BSc) – Measurements and simulations for MRI-PET – Nuhro Ego.pdf

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Semester Project at CERN (BSc) - Measurements and simulations for MRI-PET - Nuhro Ego.pdf

Abstract

The general project of the electronics and detector group of the Institute of Particle Physics at CERN is the construction of a PET insert for a pre-clinical MRI system. For this, simulations have to be performed in GATE, an open source software dedicated to numerical simulations in medical imaging based on Geant4, in order to find the most promising PET detector geometry at different parameters. To automate and systematize this simulation process, a website and webserver have been established, which are written in Python using Flask, MongoDB, PyMongo, the Flask-PyMongo extension and Jinja2 templating. From this website it is possible to add and store simulations to a database, compare simulations, produce the necessary files for the simulations and keep track of the different stages of a specific simulation. Furthermore it is possible to compare simulations and view the results of the different analysis schemes. The project provides an interesting link between applied laboratory physics, medical physics, computational physics and theoretical particle physics.

Contents

1 Introduction 3 2 Simulations 4 2.1 Geant4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2 GATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.3 Simulations so far . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3 Aims & Ideas 6 3.1 Aims . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 3.2 Idea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 4 Realization 7 4.1 Flask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 4.2 Jinja2 template engine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 4.3 MongoDB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 4.4 Flask-PyMongo extension for Flask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 4.5 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 5 Outlook & ToDos 15 6 Conclusion 16 A List of Figures 17 B List of Listings 17 C Listings 18 C.1 GATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 C.2 Webserver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 D References 59