Final Activity Report Summary - REALTIME 3D IMAGING (Methods for Real Time 3D tomography in tissue)
The incoming fellowship offered the fellow the unique opportunity to be involved into research carried out in frames of integrated project on molecular imaging ('Integrated technologies for in-vivo molecular imaging', LSHG-CT-2003-503259), which was coordinated by the Foundation of Research and Technology, Institute of Electronic Structures and Lasers (FORTH-IESL). The fellow worked in a multinational multidisciplinary research group with the three-dimensional optical tomographer for imaging in-vivo molecular function and gene expression in large animals, such as mice, which was developed through support from the integrated project on molecular imaging.
Regular group meetings and trainings on the project allowed learning a background of noncontact methods of measurements in application to small animals, specificity of experimental data collection and difficulties associated with a problem of image reconstruction. The collaboration existing in FORTH between IESL, the Institute of Molecular Biology and Biotechnology (IMBB) and the Institute of Computer Science (ICS), as well as lectures and colloquiums were devoted to modern problems and challenges in physics, biology and computer science, whose elaboration regularly took place in FORTH and was presented by leading scientist in these fields around the world, provided broadening knowledge in molecular biology and metabolism of living biotissues as well as in novel methods and modern languages of technical computing and novel methods for three-dimensional imaging. Therefore, the fellowship offered the real opportunity to develop the fellow's career as an independent researcher at an international level and an expert in Optical tomography (OT), as well as to establish contact with the scientific and academic communities of Greece and around the world.
One of the main objectives of the fellowship was to develop novel imaging approaches applicable to the three-dimensional optical tomographer for imaging carcinogenic tumours in mice targeted by fluorescent dies or proteins. The task related to this was to reconstruct a map of distribution of optical properties inside an object with complex internal structure from measurements taken on its surface. To achieve the objectives the subsequently described work was performed.
Firstly, an analytical review of modern methods for solving Radiative transfer equation (RTE) and its diffusion approximation was carried out. Special attention was paid to mimicking boundary conditions for arbitrary geometries, to hybrid RTE-diffusion models and to the presence of internal fluorescence sources. Matlab codes were designed, simulating relative shadows caused by fluorescent inserts in a slab via numerical solution of the diffusion equation using the finite element method with a grid of variant density.
The fast 'pseudoinverse' analytic Photon average trajectory (PAT) method, in the elaboration of which the fellow took an active part, was chosen to solve the inverse problem. Proper conditions of PAT application to describe fluorescence transmittance in strongly scattering object were found. The PAT method was modified and realized as Matlab software for slab geometry. To enhance the resolution, a new method was designed based on the post-reconstruction restoration of tomograms. The application of original methods of image restoration and interpretation allowed to considerably improving the image quality, especially for inserts located near the boundary, and increased the depth spatial resolution up two times.
The research was carried out in collaboration and cooperation with leading experts in different disciplines from the host institution in Crete, Greece, from various institutions in Russia, such as the Research Institute of Laser Physics, St. Petersburg, the St. Petersburg State University, the Russian Federal Nuclear Centre in Snezhinsk, the Chernyshevsky State University in Saratov, the Institute of Applied Physics of the Russian Academy of Science in Nizhny Novgorod, from the Cranfield University, United Kingdom and, finally, from the University of Pennsylvania, in Philadelphia, United States of America. During the time of the fellowship, the fellow was involved in writing proposals and grants improving her skills in management of scientific projects and strengthening collaboration links.
Regular group meetings and trainings on the project allowed learning a background of noncontact methods of measurements in application to small animals, specificity of experimental data collection and difficulties associated with a problem of image reconstruction. The collaboration existing in FORTH between IESL, the Institute of Molecular Biology and Biotechnology (IMBB) and the Institute of Computer Science (ICS), as well as lectures and colloquiums were devoted to modern problems and challenges in physics, biology and computer science, whose elaboration regularly took place in FORTH and was presented by leading scientist in these fields around the world, provided broadening knowledge in molecular biology and metabolism of living biotissues as well as in novel methods and modern languages of technical computing and novel methods for three-dimensional imaging. Therefore, the fellowship offered the real opportunity to develop the fellow's career as an independent researcher at an international level and an expert in Optical tomography (OT), as well as to establish contact with the scientific and academic communities of Greece and around the world.
One of the main objectives of the fellowship was to develop novel imaging approaches applicable to the three-dimensional optical tomographer for imaging carcinogenic tumours in mice targeted by fluorescent dies or proteins. The task related to this was to reconstruct a map of distribution of optical properties inside an object with complex internal structure from measurements taken on its surface. To achieve the objectives the subsequently described work was performed.
Firstly, an analytical review of modern methods for solving Radiative transfer equation (RTE) and its diffusion approximation was carried out. Special attention was paid to mimicking boundary conditions for arbitrary geometries, to hybrid RTE-diffusion models and to the presence of internal fluorescence sources. Matlab codes were designed, simulating relative shadows caused by fluorescent inserts in a slab via numerical solution of the diffusion equation using the finite element method with a grid of variant density.
The fast 'pseudoinverse' analytic Photon average trajectory (PAT) method, in the elaboration of which the fellow took an active part, was chosen to solve the inverse problem. Proper conditions of PAT application to describe fluorescence transmittance in strongly scattering object were found. The PAT method was modified and realized as Matlab software for slab geometry. To enhance the resolution, a new method was designed based on the post-reconstruction restoration of tomograms. The application of original methods of image restoration and interpretation allowed to considerably improving the image quality, especially for inserts located near the boundary, and increased the depth spatial resolution up two times.
The research was carried out in collaboration and cooperation with leading experts in different disciplines from the host institution in Crete, Greece, from various institutions in Russia, such as the Research Institute of Laser Physics, St. Petersburg, the St. Petersburg State University, the Russian Federal Nuclear Centre in Snezhinsk, the Chernyshevsky State University in Saratov, the Institute of Applied Physics of the Russian Academy of Science in Nizhny Novgorod, from the Cranfield University, United Kingdom and, finally, from the University of Pennsylvania, in Philadelphia, United States of America. During the time of the fellowship, the fellow was involved in writing proposals and grants improving her skills in management of scientific projects and strengthening collaboration links.