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Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 1, Iss. 1 — Aug. 2, 2010
  • pp: 87–96

Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography

Udo Jochen Birk, Matthias Rieckher, Nikos Konstantinides, Alex Darrell, Ana Sarasa-Renedo, Heiko Meyer, Nektarios Tavernarakis, and Jorge Ripoll  »View Author Affiliations

Biomedical Optics Express, Vol. 1, Issue 1, pp. 87-96 (2010)

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The application of optical projection tomography to in-vivo experiments is limited by specimen movement during the acquisition. We present a set of mathematical correction methods applied to the acquired data stacks to correct for movement in both directions of the image plane. These methods have been applied to correct experimental data taken from in-vivo optical projection tomography experiments in Caenorhabditis elegans. Successful reconstructions for both fluorescence and white light (absorption) measurements are shown. Since no difference between movement of the animal and movement of the rotation axis is made, this approach at the same time removes artifacts due to mechanical drifts and errors in the assumed center of rotation.

© 2010 OSA

OCIS Codes
(100.6950) Image processing : Tomographic image processing
(170.6960) Medical optics and biotechnology : Tomography
(110.3010) Imaging systems : Image reconstruction techniques

ToC Category:
Image Reconstruction and Inverse Problems

Original Manuscript: May 28, 2010
Revised Manuscript: June 27, 2010
Manuscript Accepted: June 30, 2010
Published: July 14, 2010

Virtual Issues
Bio-Optics in Clinical Application, Nanotechnology, and Drug Discovery (2010) Biomedical Optics Express

Udo Jochen Birk, Matthias Rieckher, Nikos Konstantinides, Alex Darrell, Ana Sarasa-Renedo, Heiko Meyer, Nektarios Tavernarakis, and Jorge Ripoll, "Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography," Biomed. Opt. Express 1, 87-96 (2010)

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  1. M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006). [CrossRef] [PubMed]
  2. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006). [CrossRef] [PubMed]
  3. S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006). [CrossRef] [PubMed]
  4. L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009). [CrossRef] [PubMed]
  5. D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007). [CrossRef] [PubMed]
  6. D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009). [PubMed]
  7. N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010). [CrossRef] [PubMed]
  8. W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990). [CrossRef] [PubMed]
  9. C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009). [CrossRef] [PubMed]
  10. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002). [CrossRef] [PubMed]
  11. J. Sharpe, “Optical projection tomography,” Annu. Rev. Biomed. Eng. 6(1), 209–228 (2004). [CrossRef] [PubMed]
  12. M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008). [CrossRef] [PubMed]
  13. A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008). [CrossRef] [PubMed]
  14. H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).
  15. C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008). [CrossRef] [PubMed]
  16. J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004). [CrossRef] [PubMed]
  17. R. B. Schulz, J. Ripoll, and V. Ntziachristos, “Noncontact optical tomography of turbid media,” Opt. Lett. 28(18), 1701–1703 (2003). [CrossRef] [PubMed]
  18. A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, and J. Ripoll, “Source intensity profile in noncontact optical tomography,” Opt. Lett. 35(1), 34–36 (2010). [CrossRef]
  19. J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008). [CrossRef] [PubMed]
  20. J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008). [CrossRef] [PubMed]
  21. C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009). [PubMed]
  22. A. Bassi, D. Brida, C. D'Andrea, G. Valentini, S. De Silvestri, G. Cerullo, and R. Cubeddu, “Time gated optical projection tomography for 3D imaging of highly scattering biological models,” in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010), p. BTuF5.
  23. J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007). [CrossRef] [PubMed]
  24. U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.
  25. A. Katsevich, “An accurate approximate algorithm for motion compensation in two-dimensional tomography,” Inverse Probl. 26(6), 065007 (2010). [CrossRef]
  26. U. J. Birk, A. Darrell, N. Konstantinides, and J. Ripoll, “Correction of Lateral Movement and Spherical Aberrations in Optical Projection Tomography,” in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010), p. BTuF6.
  27. S. Brenner, “The genetics of Caenorhabditis elegans,” Genetics 77(1), 71–94 (1974). [PubMed]
  28. J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005). [CrossRef] [PubMed]
  29. Quantitative Imaging Group at the Faculty of Applied Sciences, Delft University of Technology, “DIPimage & DIPlib,” http://www.diplib.org/ .
  30. J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” J. Colloid Interface Sci. 179(1), 298–310 (1996). [CrossRef]
  31. L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006). [CrossRef] [PubMed]
  32. A. C. Kak, and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Service Center, 1988).
  33. D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010). [CrossRef] [PubMed]

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