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Slavomir Hudak
2006
Master's Thesis
Faculty of Mathematics, Physics and Informatics
Comenius University, Bratislava, Slovakia
This thesis provides a presentation of a parallel volume data visualization system for data supplied from confocal laser scanning microscopy. It describes and compares various methods for volume visualization and optimalization and their implementations on parallel architectures. The parallel volume renderer we have developed is implemented on a 16 nodes PC cluster connected by a high-speed Myrinet network using MPI, ray-casting and binary-swap algorithm. To improve efficiency, several optimalizations for increasing the speed of the ray casting process are used, including empty regions skipping and an efficient bricking addressing scheme. We also suggest several methods of improving the performance when using MPI and compilers. The system is capable of running interactively (several frames per second) on a PC cluster.
Keywords: Volume ray-casting, ray-tracing, parallel rendering, PC clusters, binary swap algorithm, volume data.
| Name | Description |
|---|---|
| BTF | Back-To-Front |
| CLSM | Confocal Laser Scanning Microscopy |
| CPU | Central Processing Unit |
| CT | Computed Tomography |
| FTB | Front-To-Back |
| GNU | GNU’s Not Unix (Free Software Fundation) |
| GPL | General Public Licence |
| GPU | Graphics Processor Unit |
| HPC | High Performance Clusters |
| IEEE | The Institute of Electrical and Electronics Engineers |
| ILC | International Laser Centre |
| ISO | International Standards Organization |
| I/O | Input/Output |
| LAN | Local Area Network |
| LSM | Laser Confocal Microscopy |
| MIMD | Multiple Instruction, Multiple Data |
| MISD | Multiple Instruction, Single Data |
| ILC | International Laser Centre |
| MPI | Message Passing Interface |
| MRI | Magnetic Resonance Imaging |
| NUMA | Non-Uniform Memory Access |
| RADC | Ray Acceleration by Distance Coding |
| PGI | The Portland Group, Inc. |
| PSF | Point Spread Function |
| SIMD | Single Instruction, Multiple Data |
| SISD | Single Instruction, Single Data |
| SMP | Symmetrical Multi Processing |
| SPMD | Single Program, Multiple data |
| SSE | Streaming SIMD Extensions |
| SSH | Secure Shell |
| TIFF | Tagged Image File Format |
Volume visualization is well known branch of computer graphics. To be more precise - it is part of scientific visualization area. It allows to explore internals and complex behavior of the volume objects. Mainly thanks to needs of medicine - precisely, correctly and fast enough to display organs of the human body on common personal computers - the volume visualization develops so fast. Today new techniques and available hardware make it possible to interactively visualize volume data to the doctors. Result of long research and development improved both software and hardware side of the problem. There are known and well explored techniques to visualize complex structures from various areas of science. In comparison to medicine, the structures on microscopic level are much more complex and a lot of them is still unexplored.
Recently the multidimensional visualization greatly expanded in the field of microscopy. Many techniques were successfully applied in the light or electron microscopy. Confocal laser scanning microscopy (CLSM) brings new possibilities of optical visualization that lead to rapid usage of visualization techniques for all kinds of samples.
In the first chapter we introduce the problem of interactive visualization, clarify term confocal microscopy and describe confocal data itself. Second chapter gives overview of the volume visualization methods and in detail describes idea and principles of ray tracing algorithm.