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

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Scharfe, Michael ^a,c   Pielot, Rainer ^b   Schreiber, Falk ^a,c  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b LEIBNIZ INSTITUTE FOR NEUROBIOLOGY   (Germany)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT ALGORITHMS; CELL BROADBAND ENGINE; COMPUTATIONAL PROBLEM; HETEROGENEOUS MULTICORE; HIGH-PERFORMANCE COMPUTING; MULTIMODAL REGISTRATION; OPTIMISATION METHOD; PROCESSOR ARCHITECTURES;

ALIGNMENT; BIOINFORMATICS; COMPUTER ARCHITECTURE; COST EFFECTIVENESS; HARDWARE; IMAGE ANALYSIS; IMAGE REGISTRATION; OPTIMIZATION; VISUALIZATION;

THREE DIMENSIONAL;

ALGORITHM; ARTICLE; COMPUTER ASSISTED DIAGNOSIS; IMAGE PROCESSING; METHODOLOGY; THREE DIMENSIONAL IMAGING;

ALGORITHMS; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL;

EID: 76849083607     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-20     Document Type: Article

References (31)

1. Gubatz S, Dercksen V, Brüß C, Weschke W, Wobus U. Analysis of barley (Hordeum vulgare) grain development using three-dimensional digital models. Plant Journal 2007, 52:779-790. 10.1111/j.1365-313X.2007.03260.x, 17825055.
2. Maintz J, Viergever M. A Survey of Medical Image Registration. Medical Image Analysis 1998, 2:1-36. 10.1016/S1361-8415(01)80026-8, 10638851.
3. Maes F, Collignon A, Vandermeulen D, Marchal G, Suetens P. Multimodality image registration by maximization of mutual information. IEEE Transactions on Medical Imaging 1997, 16(2):187-198. 10.1109/42.563664, 9101328.
4. Thevenanz P, Unser M. Optimization of mutual information for multiresolution image registration. IEEE Transactions on Image Processing 2000, 9(12):2083-2099. 10.1109/83.887976, 18262946.
5. Pennec X, Roche A, Cathier P, Ayache N. Non-rigid MR/US registration for tracking brain deformations. Multi-Sensor Image Fusion and its Application 2005, 107-143. CRC Press.
6. Elsen P, Pol E, Sumanaweera T, Hemler P, Napel S, Adler J. Grey value correlation techniques used for automatic matching of CT and MR brain and spine images. Visualization in Biomedical Computing, Proc. SPIE 1994, 2359:227-237.
7. Viola P, Wells W. Alignment by maximization of mutual information. International Journal of Computer Vision 1997, 24(2):137-154.
8. Pluim J, Maintz J, Viergever M. Mutual information based registration of medical images: a survey. IEEE Transactions on Medical Imaging 2003, 22:986-1004. 10.1109/TMI.2003.815867, 12906253.
9. Ohara M, Yeo H, Savino F, Iyengar G, Gong L, Inoue H, Komatsu H, Sheinin V, Daijavad S, Erickson B. Accelerating mutual-information-based linear registration on the Cell Broadband Engine Processor. IEEE International Conference on Multimedia 2007, 272-275.
10. Cooper J, Ebadollahi S, Eide E. A thin-client interface to a high performance multi-modal image analytics system. Proc. 42nd Hawaii International Conference on System Science 2009, 1-8.
11. Chen T, Raghavan R, Dale J. Cell Broadband Engine Architecture and its first implementation - a performance view. IBM Journal of Research and Development 2007, 51(5):559-572.
12. Kahle J, Day M, Hofstee H, Johns C, Maeurer T, Shippy D. Introduction to the Cell multiprocessor. IBM Journal of Research and Development 2005, 49(4/5):589-604.
13. Buttari A, Dongorra J, Kurzak J. Limitations of the PlayStation 3 for High Performance Cluster Computing. Tech. Rep. CS-07-594, University of Tennessee Computer Science 2007,
14. Maes F, Vandermeulen D, Suetens P. Medical image registration using mutual information. Proc of the IEEE 2003, 12:1699-1721.
15. Brokenshire D. Maximizing the power of the Cell Broadband Engine processor: 25 tips to optimal application performance. 2006, IBM., http://www.ibm.com/developerworks/power/library/pa-celltips1
16. Bartlett J. Programming high-performance applications on the Cell BE processor. 2007, , http://www.ibm.com/developerworks/power/library/pa-linuxps3-4
17. IBM SIMD Math Library Specification for Cell Broadband Engine Architecture, . Version 1.1 2007, IBM.
18. IBM C/C++ Language Extensions for Cell Broadband Engine Architecture, . Version 2.5 2008, IBM.
19. IBM Software Development Kit for Multicore Acceleration . Version 3.0 Programmers Guide 2008, IBM.
20. Arevalo A, Matinata R, Pandian M, Peri E, Ruby K, Thomas F, Almond C. Programming the Cell Broadband Engine Examples and Best Practices 2007, IBM, Redbooks.
21. Eichenberger A, O'Brien J, O'Brien K, Wu P, Chen T, Oden T, Prener D, Shepherd J, So B, Sura Z, Wang T, Zhang A, Zhao P, Gschwind M, Archambault R, Gao Y, Koo R. Using advanced compiler technology to exploit the performance of the Cell Broadband Engine architecture. IBM Systems Journal 2006, 45:59-84.
22. Bartlett J. An introduction to Linux on the PlayStation 3. 2007, , http://www.ibm.com/developerworks/power/library/pa-linuxps3-1
23. Gropp W, Lusk E, Skjellum A. Using MPI, portable Parallel Programming with the Message Passing Interface 1999, Cambridge, USA: MIT Press, 2.
24. The Open Access Series of Imaging Studies (OASIS). 2009, , http://www.oasis-brains.org
25. The National Institute on Aging. 2009, , http://www.nia.nih.gov/Alzheimers/Resources/HighRes.htm
26. Naishlos D. Autovectorization in GCC. 2004, Tech. rep., IBM Research Lab.
27. Insight Segmentation and Registration Toolkit (ITK). 2009, , http://www.itk.org/index.htm
28. Sachdeva V, Kistler M, Speight E, Tzeng T. Exploring the viability of the Cell Broadband Engine for bioinformatics applications. Parallel Computing 2008, 34(11):616-626.
29. Sarje A, Aluru S. Parallel genomic alignments on the Cell Broadband Engine. IEEE Transactions on Parallel and Distributed Systems 2009, 20(11):1600-1610.
30. Wirawan A, Schmidt B, Zhang H, Kwoh C. High performance protein sequence database scanning on the Cell Broadband Engine. Scientic Programming 2008, 17(1-2):97-111.
31. Junker B, Klukas C, Schreiber F. VANTED: A System for Advanced Data Analysis and Visualization in the Context of Biological Networks. BMC Bioinformatics. 2006, 7:109.