high performance computing on graphics processing units: hgpu.org

Commodity graphics hardware has become a cost-effective parallel platform to solve many general computational problems. In medical imaging and more so in digital pathology, segmentation of multiple structures on high-resolution images, is often a complex and computationally expensive task. Shape-based level set segmentation has recently emerged as a natural solution to segmenting overlapping and occluded objects. However the flexibility of the level set method has traditionally resulted in long computation times and therefore might have limited clinical utility. The processing times even for moderately sized images could run into several hours of computation time. Hence there is a clear need to accelerate these segmentations schemes. In this paper, we present a parallel implementation of a computationally heavy segmentation scheme on a graphical processing unit (GPU). The segmentation scheme incorporates level sets with shape priors to segment multiple overlapping nuclei from very large digital pathology images. We report a speedup of 19x compared to multithreaded C and MATLAB-based implementations of the same scheme, albeit with slight reduction in accuracy. Our GPU-based segmentation scheme was rigorously and quantitatively evaluated for the problem of nuclei segmentation and overlap resolution on digitized histopathology images corresponding to breast and prostate biopsy tissue specimens.