RIGID TEMPLATE REGISTRATION INMET IMAGES USING CUDA

Lennart Svensson, Johan Nysjö, Anders Brun, Ingela Nyström, Ida-Maria Sintorn

Abstract

Rigid registration is a base tool in many applications, especially in Molecular Electron Tomography (MET), and also in, e.g., registration of rigid implants in medical images and as initialization for deformable registration. As MET volumes have a low signal to noise ratio, a complete search of the six-dimensional (6D) parameter space is often employed. In this paper, we describe how rigid registration with normalized crosscorrelation can be implemented on the GPU using NVIDIA’s parallel computing architecture CUDA. We compare the performance to the Colores software and two Matlab implementations, one of which is using the GPU accelerated JACKET library. With well-aligned padding and using CUDA, the performance increases by an order of a magnitude, making it feasible to work with three-dimensional fitness landscapes, here denoted scoring volumes, that are generated on the fly. This will eventually enable the biologists to interactively register macromolecule chains in MET volumes piece by piece.

References

  1. Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., and Bournen, P. (2000). The protein data bank. Nucleic Acids Research, 28:235 - 242.
  2. Chacón, P. and Wriggers, W. (2002). Multi-resolution contour-based fitting of macromolecular structures. Journal of molecular biology, 317(3):375-384.
  3. Eaton, D. (2011). www.cs.ubc.ca/~deaton/. Accessed on Oct. 18, 2011.
  4. Harris, L. J., Larson, S. B., Hasel, K. W., and McPherson, A. (1997). Refined structure of an intact IgG2a monoclonal antibody. Biochemistry, 36(7):1581-1597.
  5. Lewis, J. P. (1995). Fast normalized cross-correlation. www.scribblethink.org/Work/nvisionInterface/nip.pdf.
  6. Pittet, J.-J., Henn, C., Engel, A., and Heymann, J. B. (1999). Visualizing 3D data obtained from microscopy on the internet. Journal of Structural Biology, 125:123-132.
  7. Sandin, S., Ofverstedt, L.-G., Wikström, A.-C., Wrange, O., and Skoglund, U. (2004). Structure and flexibility of individual immunoglobulin G molecules in solution. Structure, 12:409-415.
  8. Svensson, L., Brun, A., Nyström, I., and Sintorn, I.-M. (2011). Registration parameter spaces for molecular electron tomography images. In Image Analysis and Processing - ICIAP 2011, volume 6978 of LNCS, pages 403-412.
  9. Weber, R., Gothandaraman, A., Hinde, R., and Peterson, G. (2011). Comparing hardware accelerators in scientific applications: A case study. Parallel and Distributed Systems, IEEE Transactions on, 22(1):58 -68.
  10. Wriggers, W. (2010). Using situs for the integration of multi-resolution structures. Biophysical Reviews, 2:21-27.
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Paper Citation


in Harvard Style

Svensson L., Nysjö J., Brun A., Nyström I. and Sintorn I. (2012). RIGID TEMPLATE REGISTRATION INMET IMAGES USING CUDA . In Proceedings of the International Conference on Computer Vision Theory and Applications - Volume 1: VISAPP, (VISIGRAPP 2012) ISBN 978-989-8565-03-7, pages 418-422. DOI: 10.5220/0003844804180422


in Bibtex Style

@conference{visapp12,
author={Lennart Svensson and Johan Nysjö and Anders Brun and Ingela Nyström and Ida-Maria Sintorn},
title={RIGID TEMPLATE REGISTRATION INMET IMAGES USING CUDA},
booktitle={Proceedings of the International Conference on Computer Vision Theory and Applications - Volume 1: VISAPP, (VISIGRAPP 2012)},
year={2012},
pages={418-422},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003844804180422},
isbn={978-989-8565-03-7},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Computer Vision Theory and Applications - Volume 1: VISAPP, (VISIGRAPP 2012)
TI - RIGID TEMPLATE REGISTRATION INMET IMAGES USING CUDA
SN - 978-989-8565-03-7
AU - Svensson L.
AU - Nysjö J.
AU - Brun A.
AU - Nyström I.
AU - Sintorn I.
PY - 2012
SP - 418
EP - 422
DO - 10.5220/0003844804180422