Abstract

In recent years, three-dimensional mesoscopic imaging has gained significant importance in life sciences for fundamental studies at the whole-organ level. In this manuscript, we present an optical projection tomography (OPT) method designed for imaging of the intact mouse brain. The system features an isotropic resolution of ~50 µm and an acquisition time of four to eight minutes, using a 3-day optimized clearing protocol. Imaging of the brain autofluorescence in 3D reveals details of the neuroanatomy, while the use of fluorescent labels displays the vascular network and amyloid deposition in 5xFAD mice, an important model of Alzheimer’s disease (AD). Finally, the OPT images are compared with histological slices.

© 2017 Optical Society of America

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  1. V. Ntziachristos, “Going deeper than microscopy: the optical imaging frontier in biology,” Nat. Methods 7(8), 603–614 (2010).
    [Crossref] [PubMed]
  2. A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
    [Crossref] [PubMed]
  3. H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
    [Crossref] [PubMed]
  4. J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
    [Crossref] [PubMed]
  5. B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
    [Crossref] [PubMed]
  6. A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
    [Crossref] [PubMed]
  7. 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. Methods 7(8), 637–642 (2010).
    [Crossref] [PubMed]
  8. 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. Methods 4(4), 331–336 (2007).
    [Crossref] [PubMed]
  9. L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
    [Crossref]
  10. E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).
  11. N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
    [Crossref]
  12. E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
    [Crossref]
  13. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
    [Crossref] [PubMed]
  14. A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Press, 1988).
  15. J. Sharpe, “Optical projection tomography as a new tool for studying embryo anatomy,” J. Anat. 202(2), 175–181 (2003).
    [Crossref] [PubMed]
  16. M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
    [Crossref] [PubMed]
  17. A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
    [Crossref] [PubMed]
  18. 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]
  19. 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]
  20. 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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
    [Crossref]
  21. C. Vinegoni, D. Razansky, J.-L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
    [Crossref] [PubMed]
  22. T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
    [Crossref] [PubMed]
  23. C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J.-L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
    [Crossref]
  24. 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]
  25. A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
    [Crossref] [PubMed]
  26. C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
    [Crossref]
  27. J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
    [Crossref] [PubMed]
  28. 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 Cell 18(9), 2145–2156 (2006).
    [Crossref] [PubMed]
  29. K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
    [PubMed]
  30. T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
    [Crossref] [PubMed]
  31. T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
    [Crossref] [PubMed]
  32. S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
    [Crossref] [PubMed]
  33. J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
    [Crossref] [PubMed]
  34. J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
    [Crossref] [PubMed]
  35. H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
    [Crossref] [PubMed]
  36. S. Inoué and K. R. Spring, Video Microscopy - The Fundamentals (SpringerUS, 1997).
    [Crossref]
  37. J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
    [Crossref] [PubMed]
  38. P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70(2), 135–146 (2006).
    [Crossref] [PubMed]
  39. M.-T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16, 1154–1161 (2013).
    [Crossref] [PubMed]
  40. J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
    [Crossref] [PubMed]
  41. E. S. Lein and et al., “Genome-wide atlas of gene expression in the adult mouse brain,” Nature 445, 168–176 (2007).
    [Crossref]
  42. K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10, 508–513 (2013).
    [Crossref] [PubMed]
  43. H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
    [Crossref] [PubMed]
  44. A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
    [Crossref] [PubMed]

2017 (1)

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

2016 (1)

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

2015 (3)

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
[Crossref]

2014 (3)

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[Crossref] [PubMed]

2013 (8)

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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
[Crossref] [PubMed]

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
[Crossref] [PubMed]

M.-T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16, 1154–1161 (2013).
[Crossref] [PubMed]

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10, 508–513 (2013).
[Crossref] [PubMed]

2012 (4)

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

2011 (3)

J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[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]

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

2010 (4)

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

V. Ntziachristos, “Going deeper than microscopy: the optical imaging frontier in biology,” Nat. Methods 7(8), 603–614 (2010).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

2009 (3)

2008 (3)

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
[Crossref]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[Crossref] [PubMed]

J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
[Crossref] [PubMed]

2007 (3)

E. S. Lein and et al., “Genome-wide atlas of gene expression in the adult mouse brain,” Nature 445, 168–176 (2007).
[Crossref]

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]

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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

2006 (3)

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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70(2), 135–146 (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]

2003 (1)

J. Sharpe, “Optical projection tomography as a new tool for studying embryo anatomy,” J. Anat. 202(2), 175–181 (2003).
[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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Agarwal-Gupta, N.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Ahlgren, U.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Alanentalo, T.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[Crossref] [PubMed]

Altaf, M.

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Andersson, A.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Ando, R.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Andrews, N.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Arganda-Carreras, I.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Arranz, A.

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[Crossref] [PubMed]

A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
[Crossref] [PubMed]

Arridge, S.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

Avondo, J. J. H. Y.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[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,” Science 296(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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Bassi, A.

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.

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Bembenek, J. N.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Berry, R.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Betzig, E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

Böhme, R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Bradke, F.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Brenzel, A.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Bugeon, L.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[Crossref] [PubMed]

Calder, G. M.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

Cardona, A.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Chen, B.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Chen, L.

Chung, K.

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10, 508–513 (2013).
[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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

Coen, E. S.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

Cole, S. L.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Correia, T.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Costantini, I.

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

Coultas, L.

J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
[Crossref] [PubMed]

Craft, J.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

D’Andrea, C.

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.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[Crossref] [PubMed]

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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Davidson, M. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Dazai, J.

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Deininger, K.

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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Deisseroth, K.

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10, 508–513 (2013).
[Crossref] [PubMed]

Deussing, J. 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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Ding, W.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Disterhoft, J.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Dodt, H.-U.

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Dong, D.

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[Crossref] [PubMed]

A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
[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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Egen, J. G.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Eliceiri, K.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

English, B. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Ertürk, A.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Faissner, A.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Feng, Z.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Feruglio, P. F.

Fexon, L.

Fieramonti, L.

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.

Frankel, P.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Fransén-Pettersson, N.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

French, P. M. W.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[Crossref] [PubMed]

Frise, E.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Fritz-Laylin, L.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Fujimoto, S.

M.-T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16, 1154–1161 (2013).
[Crossref] [PubMed]

Fukami, K.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Gale, N. W.

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

Gleave, J. A.

J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Gong, H.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Grathwohl, S. A.

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

Grill, S. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Guillozet-Bongaarts, A.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Gunzer, M.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Gupta, S.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Hagemann, N.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Hama, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Hammer, J. A.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Hannibal, T. D.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Hansen, L.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Hartenstein, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Hasseldam, H.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Hellal, F.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Henkelman, R. M.

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
[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]

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]

Hermann, D. M.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Hindle, C. R.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

Hojer, C. D.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Holmberg, D.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[Crossref] [PubMed]

Hörnblad, A.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

Huisken, J.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
[Crossref]

A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
[Crossref] [PubMed]

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

Imai, T.

M.-T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16, 1154–1161 (2013).
[Crossref] [PubMed]

Inoué, S.

S. Inoué and K. R. Spring, Video Microscopy - The Fundamentals (SpringerUS, 1997).
[Crossref]

Jährling, N.

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Janetopoulos, C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Jucker, M.

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

Kak, A. C.

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Press, 1988).

Katan, M.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Kaufmann, A.

A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
[Crossref] [PubMed]

Kawano, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Kaynig, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Ke, M.-T.

M.-T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16, 1154–1161 (2013).
[Crossref] [PubMed]

Keller, P. 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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Khairy, 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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Kiehart, D. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Kumar, S.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Kumar, V.

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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

Kurokawa, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Lamb, J. R.

Larefalk, Å.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[Crossref] [PubMed]

Lee, K.

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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

Lee, K. J. I.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

Legant, W. R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Lein, E. S.

E. S. Lein and et al., “Genome-wide atlas of gene expression in the adult mouse brain,” Nature 445, 168–176 (2007).
[Crossref]

Leischner, 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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Lerch, J. P.

J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Li, A.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Liu, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Liu, Z.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Lockwood, N.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Logan, S.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Longair, M.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Lorén, C. E.

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[Crossref] [PubMed]

Lugo-Hernandez, E.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Luo, Q.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Lv, X.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Mascaro, A. L. A.

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

Mauch, C. P.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Maus, E.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Mayans, S.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

McGinty, J.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[Crossref] [PubMed]

Mickoleit, M.

A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
[Crossref] [PubMed]

Milkie, D. E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Mimori-Kiyosue, Y.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Mione, M.

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]

Mitchell, D. M.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Miyawaki, A.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Morrison, H.

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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

Mullins, R. D.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Nahrendorf, M.

Newman, J. L.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

Nieman, B. J.

J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Nilsson, A. K.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

Noda, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Ntziachristos, V.

V. Ntziachristos, “Going deeper than microscopy: the optical imaging frontier in biology,” Nat. Methods 7(8), 603–614 (2010).
[Crossref] [PubMed]

C. Vinegoni, D. Razansky, J.-L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[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. Methods 5(1), 45–47 (2008).
[Crossref]

Oakley, H.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Oehler, 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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

Ohno, M.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Pavone, F. S.

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

Perrimon, N.

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
[Crossref]

Perry, P.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Peychl, J.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
[Crossref]

Pietzsch, T.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Pitsouli, C.

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
[Crossref]

Pivovarov, M.

Pozzo, A.

Preibisch, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Qi, X.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Qin, 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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

Ramel, M.-C.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Razansky, D.

C. Vinegoni, D. Razansky, J.-L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[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. Methods 5(1), 45–47 (2008).
[Crossref]

Reymann, A.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Reynaud, E. G.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
[Crossref]

Ripoll, J.

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
[Crossref] [PubMed]

Ritter, A. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Robinson, S. N.

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

Romero, D. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Rossant, J.

J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
[Crossref] [PubMed]

Rozell, B.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Rudin, M.

Rueden, C.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Saalfeld, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Sacconi, L.

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

Sakaue-Sawano, A.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Sanchez-Mendoza, E. H.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Sardari, M.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Savakis, C.

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

Sbarbati, A.

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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Schindelin, J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Schlechter, J.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Schmid, B.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Schmidt-Christensen, A.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Seydoux, G.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Shao, L.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Shao, P.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Sharpe, J.

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[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]

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 Cell 18(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, “Optical projection tomography as a new tool for studying embryo anatomy,” J. Anat. 202(2), 175–181 (2003).
[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,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Sheng, M.

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Shimogori, T.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

Silvestri, L.

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

Slaney, M.

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Press, 1988).

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]

Spring, K. R.

S. Inoué and K. R. Spring, Video Microscopy - The Fundamentals (SpringerUS, 1997).
[Crossref]

Squire, A.

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

Stainier, D. Y. R.

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

Stein, J. V.

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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Taylor, H. B.

Thévenaz, P.

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70(2), 135–146 (2006).
[Crossref] [PubMed]

Tian, J.

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
[Crossref] [PubMed]

Tinevez, J.-Y.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Tomancak, P.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
[Crossref]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Tsatsanis, C.

Tulu, U. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Unser, M.

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70(2), 135–146 (2006).
[Crossref] [PubMed]

Utoft, R.

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

Valentini, G.

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]

Van Eldik, L.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Vassaar, R.

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Vinegoni, C.

Walls, J. R.

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
[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]

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]

Wang, J. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Wang, K.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Wang, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Weber, M.

A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
[Crossref] [PubMed]

Wegenast-Braun, B. M.

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

Weissleder, R.

White, D. J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[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. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Wong, M. D.

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Wu, J.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Wu, X. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Xu, T.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Yan, C.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Yang, Z.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Yin, J.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

Zeng, S.

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Zhang, B.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Zhu, S.

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[Crossref] [PubMed]

A. Arranz, D. Dong, S. Zhu, M. Rudin, C. Tsatsanis, J. Tian, and J. Ripoll, “Helical optical projection tomography,” Opt. Express 21(22), 25912–25925 (2013).
[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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

Development (2)

J. Huisken and D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

A. Kaufmann, M. Mickoleit, M. Weber, and J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope,” Development 139(17), 3242–3247 (2012).
[Crossref] [PubMed]

Diabetes (1)

T. Alanentalo, A. Hörnblad, S. Mayans, A. K. Nilsson, J. Sharpe, Å. Larefalk, U. Ahlgren, and D. Holmberg, “Quantification and three-dimensional imaging of the insulitis-induced destruction of β-cells in murine type 1 diabetes,” Diabetes 59(7), 1756–1764 (2010).
[Crossref] [PubMed]

IEEE J. Biomed. Health Inform. (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 J. Biomed. Health Inform. 17(1), 198–204 (2013).
[Crossref]

J. Anat. (1)

J. Sharpe, “Optical projection tomography as a new tool for studying embryo anatomy,” J. Anat. 202(2), 175–181 (2003).
[Crossref] [PubMed]

J. Biomed. Opt. (2)

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]

T. Alanentalo, C. E. Lorén, Å. Larefalk, J. Sharpe, D. Holmberg, and U. Ahlgren, “High-resolution three-dimensional imaging of islet- infiltrate interactions based on optical projection tomography assessments of the intact adult mouse pancreas,” J. Biomed. Opt. 13(5), 054070 (2008).
[Crossref] [PubMed]

J. Cereb. Blood Flow Metab. (1)

E. Lugo-Hernandez, A. Squire, N. Hagemann, A. Brenzel, M. Sardari, J. Schlechter, E. H. Sanchez-Mendoza, M. Gunzer, A. Faissner, and D. M. Hermann, “3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy,” J. Cereb. Blood Flow Metab. 0(00), 1–13 (2017).

J. Exp. Bot. (1)

K. J. I. Lee, G. M. Calder, C. R. Hindle, J. L. Newman, S. N. Robinson, J. J. H. Y. Avondo, and E. S. Coen, “Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity,” J. Exp. Bot. 68(3), 527–538 (2016).
[PubMed]

J. Neurosci. (1)

H. Oakley, S. L. Cole, S. Logan, E. Maus, P. Shao, J. Craft, A. Guillozet-Bongaarts, M. Ohno, J. Disterhoft, L. Van Eldik, R. Berry, and R. Vassaar, “Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation,” J. Neurosci. 26(40), 10129–10140 (2006).
[Crossref] [PubMed]

Methods (1)

L. Silvestri, A. L. A. Mascaro, I. Costantini, L. Sacconi, and F. S. Pavone, “Correlative two-photon and light sheet microscopy,” Methods 66, 268–272 (2014).
[Crossref]

Microsc. Res. Tech. (1)

P. Thévenaz and M. Unser, “User-friendly semiautomated assembly of accurate image mosaics in microscopy,” Microsc. Res. Tech. 70(2), 135–146 (2006).
[Crossref] [PubMed]

Nat. Methods (7)

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

K. Chung and K. Deisseroth, “CLARITY for mapping the nervous system,” Nat. Methods 10, 508–513 (2013).
[Crossref] [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. Methods 7(8), 637–642 (2010).
[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. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

V. Ntziachristos, “Going deeper than microscopy: the optical imaging frontier in biology,” Nat. Methods 7(8), 603–614 (2010).
[Crossref] [PubMed]

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2015).
[Crossref]

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
[Crossref]

Nat. Neurosci. (2)

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scal e: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14, 1481–1488 (2011).
[Crossref] [PubMed]

M.-T. Ke, S. Fujimoto, and T. Imai, “SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction,” Nat. Neurosci. 16, 1154–1161 (2013).
[Crossref] [PubMed]

Nat. Protoc. (1)

A. Ertürk, K. Becker, N. Jährling, C. P. Mauch, C. D. Hojer, J. G. Egen, F. Hellal, F. Bradke, M. Sheng, and H.-U. Dodt, “Three-dimensional imaging of solvent-cleared organs using 3DISCO,” Nat. Protoc. 7, 1983–1995 (2012).
[Crossref] [PubMed]

Nature (1)

E. S. Lein and et al., “Genome-wide atlas of gene expression in the adult mouse brain,” Nature 445, 168–176 (2007).
[Crossref]

Neuroimage (1)

H. Gong, S. Zeng, C. Yan, X. Lv, Z. Yang, T. Xu, Z. Feng, W. Ding, X. Qi, A. Li, J. Wu, and Q. Luo, “Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution,” Neuroimage 74, 87–98 (2013);
[Crossref] [PubMed]

Opt. Express (2)

Opt. Lett. (1)

Phys. Med. Biol. (2)

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. 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]

Physiol. Genomics (1)

J. A. Gleave, M. D. Wong, J. Dazai, M. Altaf, R. M. Henkelman, J. P. Lerch, and B. J. Nieman, “Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging,” Physiol. Genomics 44(15), 778–785 (2012).
[Crossref] [PubMed]

Plant Cell (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 Cell 18(9), 2145–2156 (2006).
[Crossref] [PubMed]

PLoS One (6)

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLoS One 10(8), e0136213 (2015).
[Crossref] [PubMed]

J. A. Gleave, J. P. Lerch, R. M. Henkelman, and B. J. Nieman, “A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells,” PLoS One 8(8), e72039 (2013).
[Crossref] [PubMed]

S. Gupta, R. Utoft, H. Hasseldam, A. Schmidt-Christensen, T. D. Hannibal, L. Hansen, N. Fransén-Pettersson, N. Agarwal-Gupta, B. Rozell, A. Andersson, and D. Holmberg, “Global and 3D spatial assessment of neuroinflammation in rodent models of multiple sclerosis,” PLoS One 8(10), e76330 (2013).
[Crossref] [PubMed]

M. D. Wong, J. Dazai, J. R. Walls, N. W. Gale, and R. M. Henkelman, “Design and Implementation of a custom built optical projection tomography system,” PLoS One 8(9), e73491 (2013).
[Crossref] [PubMed]

N. Jährling, K. Becker, B. M. Wegenast-Braun, S. A. Grathwohl, M. Jucker, and H.-U. Dodt, “Cerebral β-amyloidosis in mice investigated by ultramicroscopy,” PLoS One 10(5), e0125418 (2015).
[Crossref]

J. R. Walls, L. Coultas, J. Rossant, and R. M. Henkelman, “Three-dimensional analysis of vascular development in the mouse embryo,” PLoS One 3(8), e2853 (2008).
[Crossref] [PubMed]

Sci. Rep. (1)

A. Arranz, D. Dong, S. Zhu, C. Savakis, J. Tian, and J. Ripoll, “In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster,” Sci. Rep. 4, 7325 (2014).
[Crossref] [PubMed]

Science (3)

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref] [PubMed]

Other (2)

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Press, 1988).

S. Inoué and K. R. Spring, Video Microscopy - The Fundamentals (SpringerUS, 1997).
[Crossref]

Supplementary Material (5)

NameDescription
» Visualization 1       Video of the 3D neuroanatomy of an 8-month-old B6SJL F1 mouse brain acquired with OPT.
» Visualization 2       Video of the 3D vascular network in a 4-month-old B6SJL F1 mouse brain acquired with OPT.
» Visualization 3       Video of the 3D amyloid deposition in an 8-month-old 5xFAD mouse brain acquired with OPT.
» Visualization 4       Histology slice of a 9-month-old B6SJL F1 mouse brain whose vasculature has been labeled.
» Visualization 5       Histology slice of a 3-month-old 5xFAD mouse brain whose amyloid deposition has been labeled.

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Figures (6)

Fig. 1
Fig. 1 OPT design. The optical layout (A) and the corresponding CAD rendering (B) illustrate the detection (blue) and illumination (green) arms. A detailed view of the LEDs mount (C) demonstrates the system for alignment and switching. It is composed of a custom heat sink (yellow), a spring (red, C.254.250.0250.A, Vanel), and a ring (blue, SM1RR, Thorlabs) stacked inside a 1-inch tube (SM1L20, Thorlabs) and screwed to a quick-release translation mount (CXY1Q, Thorlabs). The custom sample holding mechanism (D) consists of a base tube (yellow) glued to a magnet (green) to hold the magnetic stainless steel cylinder (red). The sample is glued to the blue cylinder which can be screwed to the whole mechanism.
Fig. 2
Fig. 2 Image processing pipeline illustrating the filtered back-projection (FBP) as well as the automatic retrieval of the COR algorithms. After a pre-processing step (described in text), the sinograms are filtered and the corresponding COR is retrieved. Following these operations, the sinograms are back-projected to form the virtual tissue sections, and 3D rendering is applied.
Fig. 3
Fig. 3 Photograph of a mounted and cleared 8-month-old B6SJL F1 mouse brain (A). 3D rendering of the OPT image obtained from tissue autofluorescence (B, Visualization 1). Single coronal sections of the OPT image (C) showing the inner morphology of the intact organ: cc, corpus callosum; cent, central lobule; cp, caudoputamen; ctx, cerebral cortex; cul, culmen; hip, hippocampal region; ic, inferior colliculus; mm, medial mammillary nucleus; och, optic chiasm; p, pons; th, thalamus; v3, third ventricle; vl, lateral ventricle. Grid spacing (in A): 1 cm. Scale bars: 1 mm.
Fig. 4
Fig. 4 Visualization of the brain vasculature in a 4-month-old B6SJL F1 mouse. The brain was perfused with an FITC-albumin hydrogel and imaged with OPT. 3D rendering from the top (A), side (B), and bottom (C) view (see Visualization 2). Maximum intensity projections of 20 coronal sections through the whole brain (D) showing the penetrating venules/arterioles. ACA, anterior cerebral artery; CRV, caudal rhinal vein; MCA, middle cerebral artery; SS, sigmoid sinus; SSS, superior sagittal sinus. Scale bars: 1 mm.
Fig. 5
Fig. 5 3D imaging of amyloid deposition in an 8-month-old 5xFAD mouse. Single coronal sections (A) with the arrows pointing to regions with high deposition and three-dimensional rendering of the OPT image (B, Visualization 3). A 3D image of the subiculum (green) is shown within a whole mouse brain (C) to compare with the location of amyloid deposition. Image (C) was obtained from the Allen mouse brain atlas [41]. Scale bars: 1 mm.
Fig. 6
Fig. 6 Comparison of histological and OPT slices. 40 µm-coronal section of a 9-month-old B6SJL F1 mouse brain hemisphere labeled for vasculature (A, Visualization 4) and corresponding single OPT section (B). A maximum intensity projection (C) taken over 20 consecutive OPT sections, which represents approximately 0.5 mm in thickness, gives a better representation of the penetrating vessels and highlights the 3D advantage of this technique. 40 µm-coronal section of a 3-month-old 5xFAD mouse brain hemisphere labeled for plaques (D, Visualization 5) and corresponding single OPT section (E), some regions such as the corpus callosum (cc) show an inverted contrast. Scale bars: 2 mm.

Tables (1)

Tables Icon

Table 1 OPT configuration to visualize different features of interest. Stated are LEDs, filters, exposure time, and total acquisition time. Filters references are from Chroma: EX, excitation filter; DC, dichroic mirror; EM, emission filter.

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