Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets

BMC Bioinformatics

Research Article

Rainer Pielot¹  Michael Scharfe²  Falk Schreiber² 

[1] Leibniz-Institute for Neurobiology (IfN), Brenneckestr. 6, D-39118, Magdeburg, Germany;Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Gatersleben, Germany;Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, D-06120, Halle, Germany;

关键词: Message Passing Interface;    Normalise Mutual Information;    Cell Processor;    Program Listing;    Cell Broadband Engine;   

DOI  :  10.1186/1471-2105-11-20

 received in 2009-05-17, accepted in 2010-01-11,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundSolving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks.ResultsWe evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de.ConclusionsThe results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics.

【 授权许可】

Unknown   
© Scharfe et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.