Abstract

A new technique termed Helical Optical Projection Tomography (hOPT) has been developed with the aim to overcome some of the limitations of current 3D optical imaging techniques. hOPT is based on Optical Projection Tomography (OPT) with the major difference that there is a translation of the sample in the vertical direction during the image acquisition process, requiring a new approach to image reconstruction. Contrary to OPT, hOPT makes possible to obtain 3D-optical images of intact long samples without imposing limits on the sample length. This has been tested using hOPT to image long murine tissue samples such as spinal cords and large intestines. Moreover, 3D-reconstructed images of the colon of DSS-treated mice, a model for Inflammatory Bowel Disease, allowed the identification of the structural alterations. Finally, the geometry of the hOPT device facilitates the addition of a Selective Plane Illumination Microscopy (SPIM) arm, providing the possibility of delivering high resolution images of selected areas together with complete volumetric information.

© 2013 OSA

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2013 (2)

M. B. Ahrens, M. B. Orger, D. N. Robson, J. M. Li, and P. J. Keller, “Whole-brain functional imaging at cellular resolution using light-sheet microscopy,” Nat. Methods10(5), 413–420 (2013).
[CrossRef] [PubMed]

A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

2012 (7)

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

L. Chen, J. McGinty, H. B. Taylor, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “Incorporation of an experimentally determined MTF for spatial frequency filtering and deconvolution during optical projection tomography reconstruction,” Opt. Express20(7), 7323–7337 (2012).
[CrossRef] [PubMed]

2011 (7)

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt.16(10), 100502 (2011).
[CrossRef] [PubMed]

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic optical projection tomography in vivo,” PLoS ONE6(4), e18963 (2011).
[CrossRef] [PubMed]

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.50(4), 392–398 (2011).
[CrossRef] [PubMed]

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.50(4), 392–398 (2011).
[CrossRef] [PubMed]

T. V. Truong, W. Supatto, D. S. Koos, J. M. Choi, and S. E. Fraser, “Deep and fast live imaging with two-photon scanned light-sheet microscopy,” Nat. Methods8(9), 757–760 (2011).
[CrossRef] [PubMed]

A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
[PubMed]

2010 (5)

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

J. Swoger, M. Muzzopappa, H. López-Schier, and J. Sharpe, “4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies,” J. Biophotonics13, 1–13 (2010).
[PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods7(8), 637–642 (2010).
[CrossRef] [PubMed]

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods7(6), 418–419 (2010).
[CrossRef] [PubMed]

V. Ntziachristos, “Going deeper than microscopy: the optical imaging frontier in biology,” Nat. Methods7(8), 603–614 (2010).
[CrossRef] [PubMed]

2009 (4)

J.-F. Colas and J. Sharpe, “Live optical projection tomography,” Organogenesis5(4), 211–216 (2009).
[CrossRef] [PubMed]

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]

A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
[CrossRef] [PubMed]

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

2007 (7)

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]

S. Wirtz, C. Neufert, B. Weigmann, and M. F. Neurath, “Chemically induced mouse models of intestinal inflammation,” Nat. Protoc.2(3), 541–546 (2007).
[CrossRef] [PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
[PubMed]

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
[CrossRef] [PubMed]

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
[CrossRef] [PubMed]

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods5(1), 45–47 (2007).
[CrossRef] [PubMed]

L. McGurk, H. Morrison, L. P. Keegan, J. Sharpe, and M. A. O’Connell, “Three-dimensional imaging of Drosophila melanogaster,” PLoS ONE2(9), e834 (2007).
[CrossRef] [PubMed]

2006 (1)

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

2005 (1)

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]

2004 (2)

R. J. Bryson-Richardson and P. D. Currie, “Optical projection tomography for spatio-temporal analysis in the zebrafish,” Methods Cell Biol.76, 37–50 (2004).
[CrossRef] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

2002 (1)

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

1902 (1)

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Größenbestimmung ultramikoskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Ann. Phys.315(1), 1–39 (1902).
[CrossRef]

Ahlgren, U.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
[CrossRef] [PubMed]

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Ahrens, M. B.

M. B. Ahrens, M. B. Orger, D. N. Robson, J. M. Li, and P. J. Keller, “Whole-brain functional imaging at cellular resolution using light-sheet microscopy,” Nat. Methods10(5), 413–420 (2013).
[CrossRef] [PubMed]

Alanentalo, T.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
[CrossRef] [PubMed]

Androulidaki, A.

A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Arranz, A.

A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Asayesh, A.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
[CrossRef] [PubMed]

Avondo, J.

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

Baldock, R.

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Bangham, A.

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
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Bao, Z.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods7(8), 637–642 (2010).
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L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt.16(10), 100502 (2011).
[CrossRef] [PubMed]

Becker, K.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
[CrossRef] [PubMed]

Betzig, E.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Birk, U. J.

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
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M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic optical projection tomography in vivo,” PLoS ONE6(4), e18963 (2011).
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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.50(4), 392–398 (2011).
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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.50(4), 392–398 (2011).
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Blot, L.

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

Bradke, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
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Bryson-Richardson, R. J.

R. J. Bryson-Richardson and P. D. Currie, “Optical projection tomography for spatio-temporal analysis in the zebrafish,” Methods Cell Biol.76, 37–50 (2004).
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Bugeon, L.

Cerullo, G.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

Chen, L.

Chiang, A.-S.

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

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T. V. Truong, W. Supatto, D. S. Koos, J. M. Choi, and S. E. Fraser, “Deep and fast live imaging with two-photon scanned light-sheet microscopy,” Nat. Methods8(9), 757–760 (2011).
[CrossRef] [PubMed]

Coen, E.

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

Coissieux, M.-M.

A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
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J.-F. Colas and J. Sharpe, “Live optical projection tomography,” Organogenesis5(4), 211–216 (2009).
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Cotelli, F.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

Cubeddu, R.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

Currie, P. D.

R. J. Bryson-Richardson and P. D. Currie, “Optical projection tomography for spatio-temporal analysis in the zebrafish,” Methods Cell Biol.76, 37–50 (2004).
[CrossRef] [PubMed]

D’Andrea, C.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt.16(10), 100502 (2011).
[CrossRef] [PubMed]

Dallman, M. J.

Danuser, R.

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

Darrell, A.

Davidson, D.

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Davidson, M. W.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

De Silvestri, S.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

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H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
[CrossRef] [PubMed]

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J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
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A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
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A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
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H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
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A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
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A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
[PubMed]

Dodt, H. U.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Dodt, H.-U.

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
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D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
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S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

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A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
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Eder, M.

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
[CrossRef] [PubMed]

Enikolopov, G.

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

Ertürk, A.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Farrell, J.

A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
[PubMed]

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A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
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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]

Fieramonti, L.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt.16(10), 100502 (2011).
[CrossRef] [PubMed]

Figueiredo, J.-L.

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]

Fléjou, J.-F.

A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
[CrossRef] [PubMed]

Foglia, E. A.

L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

Förstner, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Fraser, S. E.

T. V. Truong, W. Supatto, D. S. Koos, J. M. Choi, and S. E. Fraser, “Deep and fast live imaging with two-photon scanned light-sheet microscopy,” Nat. Methods8(9), 757–760 (2011).
[CrossRef] [PubMed]

French, P. M. W.

Fu, Y.-Y.

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

Fukui, Y.

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

Gadot, N.

A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
[CrossRef] [PubMed]

Gao, L.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Giannikaki, E.

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

Goldstein, B.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Greger, K.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
[PubMed]

Halin, C.

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

Harrison, D. J.

A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
[PubMed]

Hecksher-Sørensen, J.

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Hellal, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Henkelman, R. M.

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).
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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).
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Higgins, C. D.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Hill, B.

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,” Science296(5567), 541–545 (2002).
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Holmberg, D.

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
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Hübener, M.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Huisken, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Ieronymaki, E.

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Jährling, N.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
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L. McGurk, H. Morrison, L. P. Keegan, J. Sharpe, and M. A. O’Connell, “Three-dimensional imaging of Drosophila melanogaster,” PLoS ONE2(9), e834 (2007).
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M. B. Ahrens, M. B. Orger, D. N. Robson, J. M. Li, and P. J. Keller, “Whole-brain functional imaging at cellular resolution using light-sheet microscopy,” Nat. Methods10(5), 413–420 (2013).
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A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
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A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
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A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
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A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

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D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
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V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
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A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
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A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
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K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
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A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
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M. B. Ahrens, M. B. Orger, D. N. Robson, J. M. Li, and P. J. Keller, “Whole-brain functional imaging at cellular resolution using light-sheet microscopy,” Nat. Methods10(5), 413–420 (2013).
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S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
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T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
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P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
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A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
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A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
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A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
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A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
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H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
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McGurk, L.

L. McGurk, H. Morrison, L. P. Keegan, J. Sharpe, and M. A. O’Connell, “Three-dimensional imaging of Drosophila melanogaster,” PLoS ONE2(9), e834 (2007).
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A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
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M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic optical projection tomography in vivo,” PLoS ONE6(4), e18963 (2011).
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L. McGurk, H. Morrison, L. P. Keegan, J. Sharpe, and M. A. O’Connell, “Three-dimensional imaging of Drosophila melanogaster,” PLoS ONE2(9), e834 (2007).
[CrossRef] [PubMed]

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
[CrossRef] [PubMed]

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

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J. Swoger, M. Muzzopappa, H. López-Schier, and J. Sharpe, “4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies,” J. Biophotonics13, 1–13 (2010).
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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).
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V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
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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]

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods5(1), 45–47 (2007).
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L. McGurk, H. Morrison, L. P. Keegan, J. Sharpe, and M. A. O’Connell, “Three-dimensional imaging of Drosophila melanogaster,” PLoS ONE2(9), e834 (2007).
[CrossRef] [PubMed]

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D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
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V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
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M. B. Ahrens, M. B. Orger, D. N. Robson, J. M. Li, and P. J. Keller, “Whole-brain functional imaging at cellular resolution using light-sheet microscopy,” Nat. Methods10(5), 413–420 (2013).
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P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
[PubMed]

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A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
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A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
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C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods5(1), 45–47 (2007).
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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,” Science296(5567), 541–545 (2002).
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C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods5(1), 45–47 (2007).
[CrossRef] [PubMed]

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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]

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L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
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D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

Qu, X.

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

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A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

Razansky, D.

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]

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods5(1), 45–47 (2007).
[CrossRef] [PubMed]

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A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

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A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Rieckher, M.

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic optical projection tomography in vivo,” PLoS ONE6(4), e18963 (2011).
[CrossRef] [PubMed]

Ripoll, J.

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
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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.50(4), 392–398 (2011).
[CrossRef] [PubMed]

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic optical projection tomography in vivo,” PLoS ONE6(4), e18963 (2011).
[CrossRef] [PubMed]

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.50(4), 392–398 (2011).
[CrossRef] [PubMed]

Robson, D. N.

M. B. Ahrens, M. B. Orger, D. N. Robson, J. M. Li, and P. J. Keller, “Whole-brain functional imaging at cellular resolution using light-sheet microscopy,” Nat. Methods10(5), 413–420 (2013).
[CrossRef] [PubMed]

Ross, A.

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Saalfeld, S.

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods7(6), 418–419 (2010).
[CrossRef] [PubMed]

Santella, A.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods7(8), 637–642 (2010).
[CrossRef] [PubMed]

Sarasa-Renedo, A.

Savakis, C.

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

Scandella, E.

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

Schierloh, A.

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
[CrossRef] [PubMed]

Schindelin, J.

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods7(6), 418–419 (2010).
[CrossRef] [PubMed]

Schmidt, A. D.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods7(8), 637–642 (2010).
[CrossRef] [PubMed]

Scoazec, J.-Y.

A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
[CrossRef] [PubMed]

Shao, L.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Sharpe, J.

J. Swoger, M. Muzzopappa, H. López-Schier, and J. Sharpe, “4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies,” J. Biophotonics13, 1–13 (2010).
[PubMed]

J.-F. Colas and J. Sharpe, “Live optical projection tomography,” Organogenesis5(4), 211–216 (2009).
[CrossRef] [PubMed]

T. Alanentalo, A. Asayesh, H. Morrison, C. E. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods4(1), 31–33 (2007).
[CrossRef] [PubMed]

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]

L. McGurk, H. Morrison, L. P. Keegan, J. Sharpe, and M. A. O’Connell, “Three-dimensional imaging of Drosophila melanogaster,” PLoS ONE2(9), e834 (2007).
[CrossRef] [PubMed]

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

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]

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,” Science296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Sibley, E.

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

Siedentopf, H.

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Größenbestimmung ultramikoskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Ann. Phys.315(1), 1–39 (1902).
[CrossRef]

Sled, J. G.

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]

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]

Spiliopoulos, G.

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

Stark, M.

K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, “Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography,” Plant Cell18(9), 2145–2156 (2006).
[CrossRef] [PubMed]

Stathopoulos, E. N.

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Steffens, H.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med.18(1), 166–171 (2011).
[CrossRef] [PubMed]

Stein, J. V.

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

Stelzer, E. H.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Stelzer, E. H. K.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods7(8), 637–642 (2010).
[CrossRef] [PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
[PubMed]

Supatto, W.

T. V. Truong, W. Supatto, D. S. Koos, J. M. Choi, and S. E. Fraser, “Deep and fast live imaging with two-photon scanned light-sheet microscopy,” Nat. Methods8(9), 757–760 (2011).
[CrossRef] [PubMed]

Svrcek, M.

A. Paradisi, C. Maisse, M.-M. Coissieux, N. Gadot, F. Lépinasse, C. Delloye-Bourgeois, J.-G. Delcros, M. Svrcek, C. Neufert, J.-F. Fléjou, J.-Y. Scoazec, and P. Mehlen, “Netrin-1 up-regulation in inflammatory bowel diseases is required for colorectal cancer progression,” Proc. Natl. Acad. Sci. U.S.A.106(40), 17146–17151 (2009).
[CrossRef] [PubMed]

Swoger, J.

J. Swoger, M. Muzzopappa, H. López-Schier, and J. Sharpe, “4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies,” J. Biophotonics13, 1–13 (2010).
[PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
[PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Tang, S.-C.

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

Tavernarakis, N.

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic optical projection tomography in vivo,” PLoS ONE6(4), e18963 (2011).
[CrossRef] [PubMed]

Taylor, H. B.

Tian, J.

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

Tomancak, P.

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods7(6), 418–419 (2010).
[CrossRef] [PubMed]

Tosca, A.

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

Truong, T. V.

T. V. Truong, W. Supatto, D. S. Koos, J. M. Choi, and S. E. Fraser, “Deep and fast live imaging with two-photon scanned light-sheet microscopy,” Nat. Methods8(9), 757–760 (2011).
[CrossRef] [PubMed]

Tsatsanis, C.

A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Tsichlis, P. N.

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

V Stein, J.

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

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L. Fieramonti, A. Bassi, E. A. Foglia, A. Pistocchi, C. D’Andrea, G. Valentini, R. Cubeddu, S. De Silvestri, G. Cerullo, and F. Cotelli, “Time-gated optical projection tomography allows visualization of adult zebrafish internal structures,” PLoS ONE7(11), e50744 (2012).
[CrossRef] [PubMed]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt.16(10), 100502 (2011).
[CrossRef] [PubMed]

Vaporidi, K.

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Venihaki, M.

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Vergadi, E.

A. Arranz, C. Doxaki, E. Vergadi, Y. Martinez de la Torre, K. Vaporidi, E. D. Lagoudaki, E. Ieronymaki, A. Androulidaki, M. Venihaki, A. N. Margioris, E. N. Stathopoulos, P. N. Tsichlis, and C. Tsatsanis, “Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization,” Proc. Natl. Acad. Sci. U.S.A.109(24), 9517–9522 (2012).
[CrossRef] [PubMed]

Verveer, P. J.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. K. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods4(4), 311–313 (2007).
[PubMed]

Vinegoni, C.

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]

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods5(1), 45–47 (2007).
[CrossRef] [PubMed]

Walls, J. R.

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]

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]

Wedden, S. E.

A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
[PubMed]

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S. Wirtz, C. Neufert, B. Weigmann, and M. F. Neurath, “Chemically induced mouse models of intestinal inflammation,” Nat. Protoc.2(3), 541–546 (2007).
[CrossRef] [PubMed]

Weissleder, R.

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]

Wirtz, S.

S. Wirtz, C. Neufert, B. Weigmann, and M. F. Neurath, “Chemically induced mouse models of intestinal inflammation,” Nat. Protoc.2(3), 541–546 (2007).
[CrossRef] [PubMed]

Wittbrodt, J.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods7(8), 637–642 (2010).
[CrossRef] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Wu, X.

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Zacharakis, G.

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

Zacharioudaki, V.

A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

Zhu, S.

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

Zieglgänsberger, W.

H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods4(4), 331–336 (2007).
[CrossRef] [PubMed]

Zsigmondy, R.

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Größenbestimmung ultramikoskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Ann. Phys.315(1), 1–39 (1902).
[CrossRef]

Ann. Phys. (1)

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Größenbestimmung ultramikoskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Ann. Phys.315(1), 1–39 (1902).
[CrossRef]

Appl. Opt. (2)

Blood (1)

V. Kumar, E. Scandella, R. Danuser, L. Onder, M. Nitschké, Y. Fukui, C. Halin, B. Ludewig, and J. V. Stein, “Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway,” Blood115(23), 4725–4733 (2010).
[CrossRef] [PubMed]

Cell (1)

L. Gao, L. Shao, C. D. Higgins, J. S. Poulton, M. Peifer, M. W. Davidson, X. Wu, B. Goldstein, and E. Betzig, “Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens,” Cell151(6), 1370–1385 (2012).
[CrossRef] [PubMed]

Gastroenterology (1)

Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, “Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution,” Gastroenterology137(2), 453–465 (2009).
[CrossRef] [PubMed]

IEEE Trans. Inf. Technol. Biomed. (1)

D. Dong, S. Zhu, C. Qin, V. Kumar, J. V Stein, S. Oehler, C. Savakis, J. Tian, and J. Ripoll, “Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering,” IEEE Trans. Inf. Technol. Biomed.17, 198–204 (2012).
[PubMed]

IEEE Trans. Med. Imaging (1)

S. Zhu, D. Dong, U. J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, and J. Ripoll, “Automated motion correction for in vivo optical projection tomography,” IEEE Trans. Med. Imaging31(7), 1358–1371 (2012).
[CrossRef] [PubMed]

J. Biomed. Opt. (2)

A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, “Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography,” J. Biomed. Opt.17(6), 066004 (2012).
[CrossRef] [PubMed]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt.16(10), 100502 (2011).
[CrossRef] [PubMed]

J. Biophotonics (1)

J. Swoger, M. Muzzopappa, H. López-Schier, and J. Sharpe, “4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies,” J. Biophotonics13, 1–13 (2010).
[PubMed]

J. Control. Release (1)

A. Arranz, C. Reinsch, K. A. Papadakis, A. Dieckmann, U. Rauchhaus, A. Androulidaki, V. Zacharioudaki, A. N. Margioris, C. Tsatsanis, and S. Panzner, “Treatment of experimental murine colitis with CD40 antisense oligonucleotides delivered in amphoteric liposomes,” J. Control. Release165(3), 163–172 (2013).
[CrossRef] [PubMed]

J. Vis. Exp. (2)

A. D. Leeper, J. Farrell, J. M. Dixon, S. E. Wedden, D. J. Harrison, and E. Katz, “Long-term culture of human breast cancer specimens and their analysis using optical projection tomography,” J. Vis. Exp.53(53), 3085 (2011).
[PubMed]

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]

Methods Cell Biol. (1)

R. J. Bryson-Richardson and P. D. Currie, “Optical projection tomography for spatio-temporal analysis in the zebrafish,” Methods Cell Biol.76, 37–50 (2004).
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Nat. Med. (1)

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Supplementary Material (1)

» Media 1: AVI (7071 KB)     

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Figures (5)

Fig. 1
Fig. 1

Description of the hOPT set-up (a, b and c), its main components consisting of a detection objective (OLd), a tube lens (TL), an emission filter (Fd), an iris (I) which is projected to an EMCCD camera, an excitation source (LED1) and an excitation filter (Fi) and a white light (LED2) with a diffusor (D). Note that for simplicity LED2 has not been included in (a) and (b), its position being behind the bath (B) as shown in (c). The SPIM arm consists of a 473nm laser, mirrors (M), a cylindrical lens (CL) and an excitation objective (OLi). The rotation/translation module enables simultaneous rotation and translation (d). When required, samples (S) were imaged in a BABB bath (B). More details about the description of the set-up can be found in Section 2.1.

Fig. 2
Fig. 2

In order to compare hOPT with the results obtained by stitching OPT segments, a numerical simulation was performed considering a fluorescent cylinder of L/5 diameter and 4L in height as test object, as shown in (a), using a field of view of LxL. (b) Results for hOPT and stitched-OPT for the case of no photobleaching. (c) Results for hOPT for linear photobleaching of 20% per full rotation. (d), (e) and (f) Results for stitched-OPT with 10%, 25% and 50% overlap, respectively, for a linear photobleaching of 20% per full rotation. (g) Plots through the axis of the cylinder for the cases shown in (c)-(f).

Fig. 3
Fig. 3

Different samples were prepared and imaged as described in Section 2 in order to test the performance of the hOPT system. a) Murine colon images: (i) Volume render generated from hOPT measurements. (ii) Longitudinal slice through the center of the volume, where the transverse mucosal folds (TMF) can be distinguished in the proximal colon. (iii) Transversal hOPT slices from the positions shown by green arrowheads. (iv) SPIM measurements from the same positions shown in (iii), validating the 3D reconstructed images obtained by hOPT (see full stack in Media 1). (v) SPIM measurements at two different depths of the area shown in the white box of (ii); in magenta, staining with propidium iodide and in green, staining with AF488 Phalloidin. b) Volume render generated from hOPT measurements of two mouse spinal cords (i) and (ii), showing below a transversal view of (ii), where the grey and white matters (GM and WM) can be distinguished. (iii) Shows a 35 mm piece of murine small intestine. (Media 1)

Fig. 4
Fig. 4

A 20mm piece of a mouse small intestine containing a Peyer’s Patch was obtained, stained, mounted and imaged as described in Materials and Methods. (a) Coronal, sagittal and transversal hOPT slices showing the B-cell follicles present in the Peyer’s Patch. b) 3D volume render. (c) Details of the small intestine mucosa from a hOPT reconstruction compared to the same selected area imaged with SPIM (d).

Fig. 5
Fig. 5

The DSS model of colitis was established in C57BL/6 mice. Colons were obtained from healthy and DSS-treated animals and samples were prepared and imaged as described in Materials and Methods (Section 2). a) Volume render of a whole mouse colon from a DSS treated animal and (b) open volume renders of two DSS (asterisks indicate same colon sample) and one healthy (ct - control) mouse colon, including coronal slices of the area marked with the green arrowheads in (c). Tissue alteration in the inflamed mouse colon due to disruption of the villus structure can be observed in the 3D reconstructed data.

Tables (1)

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Table 1 Comparison of computation times

Equations (2)

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v rot 2π T exp N rot min ,(rad/s)
v y FO V y T exp N rot min ,(mm/s)

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