Abstract

Optical coherence tomography (OCT) allows imaging dynamic structures and fluid flow within scattering tissue, such as the beating heart and blood flow in murine embryos. For any given system, the frame rate, spatial resolution, field-of-view (FOV), and signal-to-noise ratio (SNR) are interconnected: favoring one aspect limits at least one of the others due to optical, instrumentation, and software constraints. Here we describe a spatio-temporal mosaicing technique to reconstruct high-speed, high spatial-resolution, and large-field-of-view OCT sequences. The technique is applicable to imaging any cyclically moving structure and operates on multiple, spatially overlapping tiled image sequences (each sequence acquired sequentially at a given spatial location) and effectively decouples the (rigid) spatial alignment and (non-rigid) temporal registration problems. Using this approach we reconstructed full-frame OCT sequences of the beating embryonic rat heart (11.5 days post coitus) and compared it to direct imaging on the same system, demonstrating a six-fold improvement of the frame rate without compromising spatial resolution, FOV, or SNR.

© 2011 OSA

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  5. K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]

2011

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

2010

2009

T. Schmoll, C. Kolbitsch, and R. A. Leitgeb, “Ultra-high-speed volumetric tomography of human retinal blood flow,” Opt. Express 17, 4166–4176 (2009).
[CrossRef] [PubMed]

I. Larina, S. Ivers, S. Syed, M. Dickinson, and K. Larin, “Hemodynamic measurements from individual blood cells in early mammalian embryos with Doppler swept source OCT,” Opt. Lett. 34, 986–988 (2009).
[CrossRef] [PubMed]

M. Gargesha, M. W. Jenkins, D. L. Wilson, and A. M. Rollins, “High temporal resolution OCT using image-based retrospective gating,” Opt. Express 17, 10786–10799 (2009).
[CrossRef] [PubMed]

S. Bhat, I. V. Larina, K. V. Larin, M. E. Dickinson, and M. Liebling, “Multiple-cardiac-cycle noise reduction in dynamic optical coherence tomography of the embryonic heart and vasculature,” Opt. Lett. 34, 3704–3706 (2009).
[CrossRef] [PubMed]

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
[CrossRef] [PubMed]

A. Liu, R. Wang, K. Thornburg, and S. Rugonyi, “Efficient postacquisition synchronization of 4-D nongated cardiac images obtained from optical coherence tomography: application to 4-D reconstruction of the chick embryonic heart,” J. Biomed. Opt. 14, 044020 (2009).
[CrossRef] [PubMed]

2008

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J . 2, 143–155 (2008).
[CrossRef]

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

2007

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70, 135–146 (2007).
[CrossRef]

2006

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

2005

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

D. Perperidis, R. H. Mohiaddin, and D. Rueckert, “Spatio-temporal free-form registration of cardiac MR image sequences,” Med. Image Anal. 9, 441–456 (2005).
[CrossRef] [PubMed]

2002

A. Frangi, D. Rueckert, J. Schnabel, and W. Niessen, “Automatic construction of multiple-object three-dimensional statistical shape models: Application to cardiac modeling,” IEEE Trans. Med. Imaging 21, 1151–1166 (2002).
[CrossRef]

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

A. Can, C. Stewart, B. Roysam, and H. Tanenbaum, “A feature-based technique for joint, linear estimation of high-order image-to-mosaic transformations: Mosaicing the curved human retina,” IEEE Trans. Pattern Anal. 24, 412–419 (2002).
[CrossRef]

2000

H. Shum and R. Szeliski, “Systems and experiment paper: Construction of panoramic image mosaics with global and local alignment,” Int. J. Comput. Vis. 36, 101–130 (2000).
[CrossRef]

1999

H. Sawhney and R. Kumar, “True multi-image alignment and its application to mosaicing and lens distortion correction,” IEEE Trans. Pattern Anal. 21, 235–243 (1999).
[CrossRef]

1998

P. Thévenaz, U. E. Ruttimann, and M. Unser, “A pyramid approach to subpixel registration based on intensity,” IEEE Trans. Image Process. 7, 27–41 (1998).
[CrossRef]

Ankerhold, R.

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

Bas, E.

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

Bhat, S.

Biedermann, B. R.

Burkhardt, H.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Cable, A.

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Can, A.

A. Can, C. Stewart, B. Roysam, and H. Tanenbaum, “A feature-based technique for joint, linear estimation of high-order image-to-mosaic transformations: Mosaicing the curved human retina,” IEEE Trans. Pattern Anal. 24, 412–419 (2002).
[CrossRef]

Carbajal, E. F.

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

Choma, M.

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

Dickinson, M.

I. Larina, S. Ivers, S. Syed, M. Dickinson, and K. Larin, “Hemodynamic measurements from individual blood cells in early mammalian embryos with Doppler swept source OCT,” Opt. Lett. 34, 986–988 (2009).
[CrossRef] [PubMed]

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Dickinson, M. E.

S. Bhat, I. V. Larina, K. V. Larin, M. E. Dickinson, and M. Liebling, “Multiple-cardiac-cycle noise reduction in dynamic optical coherence tomography of the embryonic heart and vasculature,” Opt. Lett. 34, 3704–3706 (2009).
[CrossRef] [PubMed]

K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
[CrossRef] [PubMed]

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

Dobnikar, A.

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

Driever, W.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Drobne, D.

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

Eigenwillig, C. M.

Emmenlauer, M.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Erdogmus, D.

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

Filippi, A.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Forouhar, A. S.

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

Frangi, A.

A. Frangi, D. Rueckert, J. Schnabel, and W. Niessen, “Automatic construction of multiple-object three-dimensional statistical shape models: Application to cardiac modeling,” IEEE Trans. Med. Imaging 21, 1151–1166 (2002).
[CrossRef]

Fraser, S. E.

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J . 2, 143–155 (2008).
[CrossRef]

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

Gargesha, M.

Gharib, M.

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

Ghosn, M.

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Griffa, A.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Huber, R.

Ivers, S.

Izatt, J.

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

Jenkins, M. W.

Jiang, J.

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Kirby, M.

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

Klein, T.

Kolbitsch, C.

Kumar, R.

H. Sawhney and R. Kumar, “True multi-image alignment and its application to mosaicing and lens distortion correction,” IEEE Trans. Pattern Anal. 21, 235–243 (1999).
[CrossRef]

Larin, K.

I. Larina, S. Ivers, S. Syed, M. Dickinson, and K. Larin, “Hemodynamic measurements from individual blood cells in early mammalian embryos with Doppler swept source OCT,” Opt. Lett. 34, 986–988 (2009).
[CrossRef] [PubMed]

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Larin, K. V.

K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
[CrossRef] [PubMed]

S. Bhat, I. V. Larina, K. V. Larin, M. E. Dickinson, and M. Liebling, “Multiple-cardiac-cycle noise reduction in dynamic optical coherence tomography of the embryonic heart and vasculature,” Opt. Lett. 34, 3704–3706 (2009).
[CrossRef] [PubMed]

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

Larina, I.

I. Larina, S. Ivers, S. Syed, M. Dickinson, and K. Larin, “Hemodynamic measurements from individual blood cells in early mammalian embryos with Doppler swept source OCT,” Opt. Lett. 34, 986–988 (2009).
[CrossRef] [PubMed]

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Larina, I. V.

K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
[CrossRef] [PubMed]

S. Bhat, I. V. Larina, K. V. Larin, M. E. Dickinson, and M. Liebling, “Multiple-cardiac-cycle noise reduction in dynamic optical coherence tomography of the embryonic heart and vasculature,” Opt. Lett. 34, 3704–3706 (2009).
[CrossRef] [PubMed]

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

Leitgeb, R. A.

Liebling, M.

S. Bhat, I. V. Larina, K. V. Larin, M. E. Dickinson, and M. Liebling, “Multiple-cardiac-cycle noise reduction in dynamic optical coherence tomography of the embryonic heart and vasculature,” Opt. Lett. 34, 3704–3706 (2009).
[CrossRef] [PubMed]

K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
[CrossRef] [PubMed]

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J . 2, 143–155 (2008).
[CrossRef]

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

Liu, A.

A. Liu, R. Wang, K. Thornburg, and S. Rugonyi, “Efficient postacquisition synchronization of 4-D nongated cardiac images obtained from optical coherence tomography: application to 4-D reconstruction of the chick embryonic heart,” J. Biomed. Opt. 14, 044020 (2009).
[CrossRef] [PubMed]

Mohiaddin, R. H.

D. Perperidis, R. H. Mohiaddin, and D. Rueckert, “Spatio-temporal free-form registration of cardiac MR image sequences,” Med. Image Anal. 9, 441–456 (2005).
[CrossRef] [PubMed]

Niessen, W.

A. Frangi, D. Rueckert, J. Schnabel, and W. Niessen, “Automatic construction of multiple-object three-dimensional statistical shape models: Application to cardiac modeling,” IEEE Trans. Med. Imaging 21, 1151–1166 (2002).
[CrossRef]

Nitschke, R.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Perperidis, D.

D. Perperidis, R. H. Mohiaddin, and D. Rueckert, “Spatio-temporal free-form registration of cardiac MR image sequences,” Med. Image Anal. 9, 441–456 (2005).
[CrossRef] [PubMed]

Ponti, A.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Rollins, A. M.

Ronneberger, O.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Roysam, B.

A. Can, C. Stewart, B. Roysam, and H. Tanenbaum, “A feature-based technique for joint, linear estimation of high-order image-to-mosaic transformations: Mosaicing the curved human retina,” IEEE Trans. Pattern Anal. 24, 412–419 (2002).
[CrossRef]

Rueckert, D.

D. Perperidis, R. H. Mohiaddin, and D. Rueckert, “Spatio-temporal free-form registration of cardiac MR image sequences,” Med. Image Anal. 9, 441–456 (2005).
[CrossRef] [PubMed]

A. Frangi, D. Rueckert, J. Schnabel, and W. Niessen, “Automatic construction of multiple-object three-dimensional statistical shape models: Application to cardiac modeling,” IEEE Trans. Med. Imaging 21, 1151–1166 (2002).
[CrossRef]

Rugonyi, S.

A. Liu, R. Wang, K. Thornburg, and S. Rugonyi, “Efficient postacquisition synchronization of 4-D nongated cardiac images obtained from optical coherence tomography: application to 4-D reconstruction of the chick embryonic heart,” J. Biomed. Opt. 14, 044020 (2009).
[CrossRef] [PubMed]

Ruttimann, U. E.

P. Thévenaz, U. E. Ruttimann, and M. Unser, “A pyramid approach to subpixel registration based on intensity,” IEEE Trans. Image Process. 7, 27–41 (1998).
[CrossRef]

Sawhney, H.

H. Sawhney and R. Kumar, “True multi-image alignment and its application to mosaicing and lens distortion correction,” IEEE Trans. Pattern Anal. 21, 235–243 (1999).
[CrossRef]

Schmoll, T.

Schnabel, J.

A. Frangi, D. Rueckert, J. Schnabel, and W. Niessen, “Automatic construction of multiple-object three-dimensional statistical shape models: Application to cardiac modeling,” IEEE Trans. Med. Imaging 21, 1151–1166 (2002).
[CrossRef]

Schwarb, P.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Shum, H.

H. Shum and R. Szeliski, “Systems and experiment paper: Construction of panoramic image mosaics with global and local alignment,” Int. J. Comput. Vis. 36, 101–130 (2000).
[CrossRef]

Stewart, C.

A. Can, C. Stewart, B. Roysam, and H. Tanenbaum, “A feature-based technique for joint, linear estimation of high-order image-to-mosaic transformations: Mosaicing the curved human retina,” IEEE Trans. Pattern Anal. 24, 412–419 (2002).
[CrossRef]

Sudheendran, N.

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

Syed, S.

Szeliski, R.

H. Shum and R. Szeliski, “Systems and experiment paper: Construction of panoramic image mosaics with global and local alignment,” Int. J. Comput. Vis. 36, 101–130 (2000).
[CrossRef]

Tanenbaum, H.

A. Can, C. Stewart, B. Roysam, and H. Tanenbaum, “A feature-based technique for joint, linear estimation of high-order image-to-mosaic transformations: Mosaicing the curved human retina,” IEEE Trans. Pattern Anal. 24, 412–419 (2002).
[CrossRef]

Thévenaz, P.

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70, 135–146 (2007).
[CrossRef]

P. Thévenaz, U. E. Ruttimann, and M. Unser, “A pyramid approach to subpixel registration based on intensity,” IEEE Trans. Image Process. 7, 27–41 (1998).
[CrossRef]

Thornburg, K.

A. Liu, R. Wang, K. Thornburg, and S. Rugonyi, “Efficient postacquisition synchronization of 4-D nongated cardiac images obtained from optical coherence tomography: application to 4-D reconstruction of the chick embryonic heart,” J. Biomed. Opt. 14, 044020 (2009).
[CrossRef] [PubMed]

Thrane, L.

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

Tuchin, V. V.

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

Unser, M.

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70, 135–146 (2007).
[CrossRef]

P. Thévenaz, U. E. Ruttimann, and M. Unser, “A pyramid approach to subpixel registration based on intensity,” IEEE Trans. Image Process. 7, 27–41 (1998).
[CrossRef]

Valant, J.

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

Vermot, J.

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J . 2, 143–155 (2008).
[CrossRef]

Wang, R.

A. Liu, R. Wang, K. Thornburg, and S. Rugonyi, “Efficient postacquisition synchronization of 4-D nongated cardiac images obtained from optical coherence tomography: application to 4-D reconstruction of the chick embryonic heart,” J. Biomed. Opt. 14, 044020 (2009).
[CrossRef] [PubMed]

Wieser, W.

Wilson, D. L.

Wolleschensky, R.

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

Yelbuz, T.

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

Zimmerman, B.

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

Zupanc, J.

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

Circulation

T. Yelbuz, M. Choma, L. Thrane, M. Kirby, and J. Izatt, “A new high-resolution imaging technology to study cardiac development in chick embryos,” Circulation 106, 2771–2774 (2002).
[CrossRef] [PubMed]

Dev. Dynam.

M. Liebling, A. S. Forouhar, R. Wolleschensky, B. Zimmerman, R. Ankerhold, S. E. Fraser, M. Gharib, and M. E. Dickinson, “Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development,” Dev. Dynam. 235, 2940–2948 (2006).
[CrossRef]

HFSP J

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J . 2, 143–155 (2008).
[CrossRef]

IEEE Trans. Image Process.

P. Thévenaz, U. E. Ruttimann, and M. Unser, “A pyramid approach to subpixel registration based on intensity,” IEEE Trans. Image Process. 7, 27–41 (1998).
[CrossRef]

IEEE Trans. Med. Imaging

A. Frangi, D. Rueckert, J. Schnabel, and W. Niessen, “Automatic construction of multiple-object three-dimensional statistical shape models: Application to cardiac modeling,” IEEE Trans. Med. Imaging 21, 1151–1166 (2002).
[CrossRef]

IEEE Trans. Pattern Anal.

H. Sawhney and R. Kumar, “True multi-image alignment and its application to mosaicing and lens distortion correction,” IEEE Trans. Pattern Anal. 21, 235–243 (1999).
[CrossRef]

A. Can, C. Stewart, B. Roysam, and H. Tanenbaum, “A feature-based technique for joint, linear estimation of high-order image-to-mosaic transformations: Mosaicing the curved human retina,” IEEE Trans. Pattern Anal. 24, 412–419 (2002).
[CrossRef]

Int. J. Comput. Vis.

H. Shum and R. Szeliski, “Systems and experiment paper: Construction of panoramic image mosaics with global and local alignment,” Int. J. Comput. Vis. 36, 101–130 (2000).
[CrossRef]

J. Biomed. Opt.

M. Liebling, A. S. Forouhar, M. Gharib, S. E. Fraser, and M. E. Dickinson, “Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences,” J. Biomed. Opt. 10, 054001 (2005).
[CrossRef] [PubMed]

A. Liu, R. Wang, K. Thornburg, and S. Rugonyi, “Efficient postacquisition synchronization of 4-D nongated cardiac images obtained from optical coherence tomography: application to 4-D reconstruction of the chick embryonic heart,” J. Biomed. Opt. 14, 044020 (2009).
[CrossRef] [PubMed]

I. Larina, N. Sudheendran, M. Ghosn, J. Jiang, A. Cable, K. Larin, and M. Dickinson, “Live imaging of blood flow in mammalian embryos using Doppler swept-source optical coherence tomography,” J. Biomed. Opt. 13, 060506 (2008).
[CrossRef]

J. Zupanc, A. Dobnikar, D. Drobne, J. Valant, D. Erdogmus, and E. Bas, “Biological reactivity of nanoparticles: mosaics from optical microscopy videos of giant lipid vesicles,” J. Biomed. Opt. 16, 026003 (2011).
[CrossRef] [PubMed]

J. Innov. Opt. Health Sci.

K. V. Larin, I. V. Larina, M. Liebling, and M. E. Dickinson, “Live imaging of early developmental processes in mammalian embryos with optical coherence tomography,” J. Innov. Opt. Health Sci. 2, 253–259 (2009).
[CrossRef] [PubMed]

J. Microsc.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233, 42–60 (2009).
[CrossRef] [PubMed]

Laser Phys. Lett.

I. V. Larina, E. F. Carbajal, V. V. Tuchin, M. E. Dickinson, and K. V. Larin, “Enhanced OCT imaging of embryonic tissue with optical clearing,” Laser Phys. Lett. 5, 476–479 (2008).
[CrossRef]

Med. Image Anal.

D. Perperidis, R. H. Mohiaddin, and D. Rueckert, “Spatio-temporal free-form registration of cardiac MR image sequences,” Med. Image Anal. 9, 441–456 (2005).
[CrossRef] [PubMed]

Microsc. Res. Tech.

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70, 135–146 (2007).
[CrossRef]

Opt. Express

Opt. Lett.

Other

M. Liebling, J. Vermot, A. Forouhar, M. Gharib, M. Dickinson, and S. Fraser, “Nonuniform temporal alignment of slice sequences for four-dimensional imaging of cyclically deforming embryonic structures,” in “Proc. ISBI 2006 ,”(2006), pp. 1156–1159.

Supplementary Material (1)

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Figures (3)

Fig. 1
Fig. 1

Tiled acquisition and automatic mosaicing procedure for dynamic images. (a) Overlapping cardiac image series, are acquired sequentially. (b) Each sequence is collapsed to a static image (temporal maximum). (c) Static images are spatially aligned. (d) Image sequences are spatially transformed and padded with zeros. (e) Spatially aligned sequences are temporally synchronized. (f) Synchronized image sequences are blended. (Color online).

Fig. 2
Fig. 2

Dynamic mosaicing overcomes frame rate, resolution, and FOV interdependence for fast SS-OCT cardiac imaging. (a) High frame rate, low spatial resolution, large FOV: 150 fps, 512×64 pixels (b) Low frame rate, high spatial resolution, large FOV, 25fps, 512×500 pixels. (c) High frame rate, high spatial resolution, small FOV (12 tiles, before dynamic mosaicing, each 150 fps, 512×64 pixels). Marks at bottom of panel indicate lateral position of individual tiles. (d) High frame rate, high spatial resolution, high FOV (after dynamic mosaicing), 150 fps, 512×500 pixels. Inserts represent time-course (500 ms total duration) of pixel intensity (arbitrary units) at location marked by arrows. SNRs were computed over rectangular boxes. Scale bars are 0.2 mm. ( Media 1).

Fig. 3
Fig. 3

Accuracy evaluation of tiled acquisition and automatic mosaicing procedure. (a) Original sequence (one of the tiles in Fig. 2(c)) is split into (b) a left tile sequence and (c) a right tile sequence. (d)–(g) Sequence subsets are registered in space and/or time. (d) Temporal alignment of first period in subsequence A to subsequence B. (e) Spatio-temporal alignment of first period in subsequence C to subsequence F. (f) Spatio-temporal alignmnent of first period in subsequence E to subsequence D. (g) Spatio-temporal alignment of first period in subsequence C to subsequence E.

Tables (1)

Tables Icon

Table 1 Registration Evaluation*

Equations (15)

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I ( x , y , t ) I ( x , y , t + T ) t ,
I n ( x , y , t ) = I ( x n + x , y , t n + t ) , 0 n < N ,
I ¯ n ( x , y ) = max 0 t < L t I n ( x , y , t ) .
x ˜ n = x ˜ n 1 + arg min 0 x < L x 0 L y 1 L x x x L x | I ¯ n ( x x , y ) I ¯ n 1 ( x , y ) | 2 d x d y ,
I n ( x , y , t ) = { 0 0 x < x ˜ n I n ( x x ˜ n , y , t ) x ˜ n x < x ˜ n + L x 0 x ˜ n + L x x < x ˜ N + L x ,
Q n { w } = λ 0 T 0 L y x ˜ n x ˜ n 1 + L x | I n 1 ( x , y , w n 1 ( t ) ) I n ( x , y , w ( t ) ) | d x d y d t + ( 1 λ ) 0 T | 1 d d t w ( t ) | d t ,
I out ( n ) ( x , y , t ) = B x ˜ n , x ˜ n 1 + L x ( x ) I out ( n 1 ) ( x , y , t ) + ( 1 B x ˜ n , x ˜ n 1 + L x ( x ) ) I n ( x , y , w n ( t ) )
B a , b ( x ) = { 1 , x < a 1 x a b a , a x b 0 , x > b .
I out ( 0 ) = I 0 ( x , y , t ) .
I out ( x , y , t ) = I out ( N 1 ) ( x , y , t ) , 0 t < T .
Δ t n W X , Y Z = 1 T 0 T | w n W X ( t ) w n Y Z ( t ) | d t ,
Δ x ˜ n W X = | x ˜ n W X x n | .
Δ x ˜ W X = 1 N n = 1 N Δ x ˜ n W X
Δ t W X , Y Z = 1 N n = 1 N Δ t n W X , Y Z .
Δ t n C E = 1 T 0 T | w n C E ( t ) t | d t .

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