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Open Access Research article

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

Michael Scharfe13, Rainer Pielot2 and Falk Schreiber13*

Author Affiliations

1 Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany

2 Leibniz-Institute for Neurobiology (IfN), Brenneckestr. 6, D-39118 Magdeburg, Germany

3 Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, D-06120 Halle, Germany

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BMC Bioinformatics 2010, 11:20  doi:10.1186/1471-2105-11-20

Published: 11 January 2010

Abstract

Background

Solving 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.

Results

We 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 webcite.

Conclusions

The 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.