high performance computing on graphics processing units: hgpu.org

In this contribution we describe a specialised data processing system for Spectral Optical Coherence Tomography (SOCT) biomedical imaging which utilises massively parallel data processing on a low-cost, Graphics Processing Unit (GPU). One of the most significant limitations of SOCT is the data processing time on the main processor of the computer (CPU), which is generally longer than the data acquisition. Therefore, real-time imaging with acceptable quality is limited to a small number of tomogram lines (A-scans). Recent progress in graphics cards technology gives a promising solution of this problem. The newest graphics processing units allow not only for a very high speed three dimensional (3D) rendering, but also for a general purpose parallel numerical calculations with efficiency higher than provided by the CPU. The presented system utilizes CUDA graphic card and allows for a very effective real time SOCT imaging. The total imaging speed for 2D data consisting of 1200 A-scans is higher than refresh rate of a 120 Hz monitor. 3D rendering of the volume data build of 10 000 A-scans is performed with frame rate of about 9 frames per second. These frame rates include data transfer from a frame grabber to GPU, data processing and 3D rendering to the screen. The software description includes data flow, parallel processing and organization of threads. For illustration we show real time high resolution SOCT imaging of human skin and eye.