Abstract

The current gold-standard histopathology for tissue analysis is destructive, time consuming, and limited to 2D slices. Light sheet microscopy has emerged as a powerful tool for 3D imaging of tissue biospecimens with its fast speed and low photo-damage, but usually with worse axial resolution and complicated configuration for sample imaging. Here, we utilized inverted selective plane illumination microscopy for easy sample mounting and imaging, and dual-view imaging and deconvolution to overcome the anisotropic resolution. We have rendered 3D images of fresh cytology cell blocks and millimeter- to centimeter-sized fixed tissue samples with high resolution in both lateral and axial directions. More accurate cellular quantification, higher image sharpness, and more image details have been achieved with the dual-view method compared with single-view imaging.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Full Article  |  PDF Article
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  1. A. H. Boag, L. A. Kennedy, and M. J. Miller, “Three-dimensional Microscopic Image Reconstruction of Prostatic Adenocarcinoma,” Arch. Pathol. Lab. Med. 125(4), 562–566 (2001).
    [PubMed]
  2. Y. Tolkach, S. Thomann, and G. Kristiansen, “Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity,” Histopathology 72(6), 1051–1059 (2018).
    [Crossref] [PubMed]
  3. M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
    [Crossref] [PubMed]
  4. A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
    [Crossref] [PubMed]
  5. D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
    [Crossref] [PubMed]
  6. S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
    [Crossref] [PubMed]
  7. O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
    [PubMed]
  8. R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
    [Crossref]
  9. W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)
  10. M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
    [Crossref] [PubMed]
  11. E. Olson, M. J. Levene, and R. Torres, “Multiphoton microscopy with clearing for three dimensional histology of kidney biopsies,” Biomed. Opt. Express 7(8), 3089–3096 (2016).
  12. Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
    [Crossref] [PubMed]
  13. J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
    [Crossref] [PubMed]
  14. R. M. Power and J. Huisken, “A guide to light-sheet fluorescence microscopy for multiscale imaging,” Nat. Methods 14(4), 360–373 (2017).
    [Crossref] [PubMed]
  15. Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
    [Crossref] [PubMed]
  16. 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]
  17. U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
    [Crossref] [PubMed]
  18. P. J. Keller, M. B. Ahrens, and J. Freeman, “Light-sheet imaging for systems neuroscience,” Nat. Methods 12(1), 27–29 (2015).
    [Crossref] [PubMed]
  19. 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]
  20. S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
    [Crossref]
  21. R. McGorty, H. Liu, D. Kamiyama, Z. Dong, S. Guo, and B. Huang, “Open-top selective plane illumination microscope for conventionally mounted specimens,” Opt. Express 23(12), 16142–16153 (2015).
    [Crossref] [PubMed]
  22. B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
    [Crossref] [PubMed]
  23. A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).
  24. A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
    [Crossref] [PubMed]
  25. B. Hu, D. Bolus, and J. Q. Brown, “Improved contrast in inverted selective plane illumination microscopy of thick tissues using confocal detection and structured illumination,” Biomed. Opt. Express 8(12), 5546–5559 (2017).
    [Crossref] [PubMed]
  26. R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
    [Crossref] [PubMed]
  27. A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).
  28. Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
    [Crossref] [PubMed]
  29. P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
    [Crossref] [PubMed]
  30. P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
    [Crossref]
  31. K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
    [Crossref] [PubMed]
  32. S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (2010).
    [Crossref] [PubMed]
  33. S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
    [Crossref] [PubMed]
  34. M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
    [Crossref] [PubMed]
  35. S. Preibisch, S. Saalfeld, and P. Tomancak, “Globally optimal stitching of tiled 3D microscopic image acquisitions,” Bioinformatics 25(11), 1463–1465 (2009).
    [Crossref] [PubMed]
  36. A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
    [Crossref] [PubMed]
  37. K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
    [Crossref] [PubMed]
  38. T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).
  39. M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
    [Crossref]
  40. P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
    [Crossref] [PubMed]

2019 (3)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

2018 (3)

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
[Crossref] [PubMed]

Y. Tolkach, S. Thomann, and G. Kristiansen, “Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity,” Histopathology 72(6), 1051–1059 (2018).
[Crossref] [PubMed]

2017 (5)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

R. M. Power and J. Huisken, “A guide to light-sheet fluorescence microscopy for multiscale imaging,” Nat. Methods 14(4), 360–373 (2017).
[Crossref] [PubMed]

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

B. Hu, D. Bolus, and J. Q. Brown, “Improved contrast in inverted selective plane illumination microscopy of thick tissues using confocal detection and structured illumination,” Biomed. Opt. Express 8(12), 5546–5559 (2017).
[Crossref] [PubMed]

2016 (8)

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

E. Olson, M. J. Levene, and R. Torres, “Multiphoton microscopy with clearing for three dimensional histology of kidney biopsies,” Biomed. Opt. Express 7(8), 3089–3096 (2016).

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

2015 (4)

P. J. Keller, M. B. Ahrens, and J. Freeman, “Light-sheet imaging for systems neuroscience,” Nat. Methods 12(1), 27–29 (2015).
[Crossref] [PubMed]

R. McGorty, H. Liu, D. Kamiyama, Z. Dong, S. Guo, and B. Huang, “Open-top selective plane illumination microscope for conventionally mounted specimens,” Opt. Express 23(12), 16142–16153 (2015).
[Crossref] [PubMed]

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

2014 (4)

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

2013 (1)

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

2012 (1)

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

2010 (2)

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (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]

2009 (2)

S. Preibisch, S. Saalfeld, and P. Tomancak, “Globally optimal stitching of tiled 3D microscopic image acquisitions,” Bioinformatics 25(11), 1463–1465 (2009).
[Crossref] [PubMed]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

2008 (1)

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

2007 (1)

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 (1)

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

2004 (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

2001 (1)

A. H. Boag, L. A. Kennedy, and M. J. Miller, “Three-dimensional Microscopic Image Reconstruction of Prostatic Adenocarcinoma,” Arch. Pathol. Lab. Med. 125(4), 562–566 (2001).
[PubMed]

Ahrens, M. B.

P. J. Keller, M. B. Ahrens, and J. Freeman, “Light-sheet imaging for systems neuroscience,” Nat. Methods 12(1), 27–29 (2015).
[Crossref] [PubMed]

Ahsen, O. O.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Amat, F.

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Antoine, M.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Apak, M. C.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Asano, S.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Assayag, O.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Bao, Z.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (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]

Barner, L.A.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Becker, 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]

Bezprozvanny, I.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Boag, A. H.

A. H. Boag, L. A. Kennedy, and M. J. Miller, “Three-dimensional Microscopic Image Reconstruction of Prostatic Adenocarcinoma,” Arch. Pathol. Lab. Med. 125(4), 562–566 (2001).
[PubMed]

Boccara, C.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Bokinsky, A.

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Bolus, D.

Boyden, E. S.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Brooker, J. S.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Brown, J. Q.

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

B. Hu, D. Bolus, and J. Q. Brown, “Improved contrast in inverted selective plane illumination microscopy of thick tissues using confocal detection and structured illumination,” Biomed. Opt. Express 8(12), 5546–5559 (2017).
[Crossref] [PubMed]

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

Burcheri, A.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Cable, A. E.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Carpenter, A. E.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Chakraborty, T.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Chandris, P.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Chang, B.-J.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Chang, J. H.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Chen, Y.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Chhetri, R. K.

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

Christensen, R.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Clarke, C.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Colombelli, J.

P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
[Crossref] [PubMed]

Colón-ramos, D.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Colón-Ramos, D. A.

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Connolly, J. L.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Dalimier, E.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Daniels, J.S.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Danuser, G.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Datta, M. S.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Dean, K. M.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

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]

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Demos, S.

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

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, Y.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Dintzis, S. M.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

Dodt, H.-U.

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

Dong, Z.

Driscoll, M.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Duncan, W.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Dupre, C.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Eastman, Z.

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

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]

Elfer, K. N.

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

Fasy, B. T.

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

Faulkner-Jones, B. E.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Fauver, M.

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Fauver, M. E.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

Fei, P.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

Fereidouni, F.

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

Fiolka, R.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Fischer, R. S.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Freeman, J.

P. J. Keller, M. B. Ahrens, and J. Freeman, “Light-sheet imaging for systems neuroscience,” Nat. Methods 12(1), 27–29 (2015).
[Crossref] [PubMed]

Friman, O.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Fujimoto, J. G.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Gandler, W.

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Gao, R.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Gareau, D. S.

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

Gerner, M.Y.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Giacomelli, M. G.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Glaser, A. K.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

Glaser, A.K.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Golland, P.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Grieve, K.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Guertin, D. A.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Gunther, S.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Guo, M.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

Guo, S.

Hagiwara, M.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Halpern, A.R.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Harmany, Z.

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

Harms, F.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Heintzmann, R.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Hermanson, O.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Hiremath, C.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Ho, C.-M.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Höckendorf, B.

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

Hori, Y.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Hornegger, J.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Houtsmuller, A. B.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

Hsiai, T. K.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Hu, B.

Huang, B.

R. McGorty, H. Liu, D. Kamiyama, Z. Dong, S. Guo, and B. Huang, “Open-top selective plane illumination microscope for conventionally mounted specimens,” Opt. Express 23(12), 16142–16153 (2015).
[Crossref] [PubMed]

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

Hufnagel, L.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Huisken, J.

R. M. Power and J. Huisken, “A guide to light-sheet fluorescence microscopy for multiscale imaging,” Nat. Methods 14(4), 360–373 (2017).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Husvogt, L.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Iijima, S.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Ikeda, J. I.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Jährling, N.

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]

Jaumouillé, V.

Johnson, N. B.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Jones, T. R.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Kamiyama, D.

Kang, I. H.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Kang, S.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Keller, P. J.

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

P. J. Keller, M. B. Ahrens, and J. Freeman, “Light-sheet imaging for systems neuroscience,” Nat. Methods 12(1), 27–29 (2015).
[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]

Kennedy, L. A.

A. H. Boag, L. A. Kennedy, and M. J. Miller, “Three-dimensional Microscopic Image Reconstruction of Prostatic Adenocarcinoma,” Arch. Pathol. Lab. Med. 125(4), 562–566 (2001).
[PubMed]

Kennel, P.

P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
[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]

Kim, E. Y.

Kimbrell, H. Z.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

Kremers, G. J.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

Kristiansen, G.

Y. Tolkach, S. Thomann, and G. Kristiansen, “Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity,” Histopathology 72(6), 1051–1059 (2018).
[Crossref] [PubMed]

Krzic, U.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Kumanogoh, A.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Kumar, A.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Kurashige, M.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Kweldam, C. F.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

La Cruz, E. D. D.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

La Riviere, P. J.

Lai, W.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

Lamprecht, M. R.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Lawson, P.

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

Le Conte de Poly, B.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Lechpammer, M.

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

Lee, B. R.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

Lee, J.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[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]

Lemon, W. C.

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

Leung, J. M.

Levene, M. J.

Levenson, R.

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

Li, S.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Li, Y.

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

Lindquist, R. A.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Liu, H.

Liu, J. T. C.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

Liu, J.T.C.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Liu, S.

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

Luethy, S.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

Maddox, M. M.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

Mandava, S. H.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

Mao, C.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Marciano, D.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Mauch, C. P.

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]

McAuliffe, M.

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

McCarty, E. F.

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

McCarty, E.F.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

McCreedy, E.

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

McGorty, R.

Meeks, J.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Meyer, M. G.

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Migliori, B.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Miller, M. J.

A. H. Boag, L. A. Kennedy, and M. J. Miller, “Three-dimensional Microscopic Image Reconstruction of Prostatic Adenocarcinoma,” Arch. Pathol. Lab. Med. 125(4), 562–566 (2001).
[PubMed]

Moffat, J.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Morii, E.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Morrison, S.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Moyle, M.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Murphy, M.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Myers, E.

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Nakahara, Y.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Nehal, K. S.

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

Nelson, A. C.

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Neumann, T.

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Nicovich, P.R.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Nie, J.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

Nielson, C.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Nojima, S.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Ohshima, K.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Olson, E.

Patten, F. W.

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Plouraboué, F.

P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
[Crossref] [PubMed]

Power, R. M.

R. M. Power and J. Huisken, “A guide to light-sheet fluorescence microscopy for multiscale imaging,” Nat. Methods 14(4), 360–373 (2017).
[Crossref] [PubMed]

Preibisch, S.

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (2010).
[Crossref] [PubMed]

S. Preibisch, S. Saalfeld, and P. Tomancak, “Globally optimal stitching of tiled 3D microscopic image acquisitions,” Bioinformatics 25(11), 1463–1465 (2009).
[Crossref] [PubMed]

Rahn, J. R.

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Rajadhyaksha, M.

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

Ramamurthi, K. S.

Reder, N. P.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

Reder, N.P.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Rey-Suarez, I.

Riben, M.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Rondeau, G.

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Roudot, P.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Saalfeld, S.

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (2010).
[Crossref] [PubMed]

S. Preibisch, S. Saalfeld, and P. Tomancak, “Globally optimal stitching of tiled 3D microscopic image acquisitions,” Bioinformatics 25(11), 1463–1465 (2009).
[Crossref] [PubMed]

Sabatini, D. M.

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Santella, A.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (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]

Sarov, M.

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Saunders, T. E.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Schierloh, A.

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

Schindelin, J.

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (2010).
[Crossref] [PubMed]

Schmidt, A. D.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Schmolze, D. B.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Segura, T.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Seibel, E. J.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

Senseney, J.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Sheikine, Y.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Shen, D.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Sholl, A. B.

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

Shroff, H.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Sigal-Zafrani, B.

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Singer, R. H.

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Smith, C.

Stamataki, E.

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Stelzer, E. H. K.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Stoltzfus, C.R.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Streichan, S. J.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Susaki, E. A.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Swoger, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Tahara, S.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Takachi, K.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Takemoto, H.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Tan, M.

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

Tao, Y. K.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Teyssedre, L.

P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
[Crossref] [PubMed]

Thomann, S.

Y. Tolkach, S. Thomann, and G. Kristiansen, “Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity,” Histopathology 72(6), 1051–1059 (2018).
[Crossref] [PubMed]

Tolkach, Y.

Y. Tolkach, S. Thomann, and G. Kristiansen, “Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity,” Histopathology 72(6), 1051–1059 (2018).
[Crossref] [PubMed]

Tomancak, P.

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (2010).
[Crossref] [PubMed]

S. Preibisch, S. Saalfeld, and P. Tomancak, “Globally optimal stitching of tiled 3D microscopic image acquisitions,” Bioinformatics 25(11), 1463–1465 (2009).
[Crossref] [PubMed]

Tomer, R.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Torres, R.

True, L. D.

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

True, L.D.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Tsujimura, N.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Tulman, D. B.

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

Ueda, H. R.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

van Cappellen, W. A.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

van Leenders, G. J. L. H.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

van Royen, M. E.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

Vardeh, H.

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Vaughan, J. C.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

Vaughan, J.C.

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Verhoef, E. I.

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

Vora, S.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Wada, N.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Wan, Y.

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

Wang, H. H.

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Wang, M.

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

Wang, Y.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

Waterman, C. M.

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Wawrzusin, P.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Wei, L.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Welf, E. S.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

Wenk, C.

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

Winter, P. W.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[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]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Wong, W. M.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Wu, Y.

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Y. Wu, P. Chandris, P. W. Winter, E. Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J. M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C. M. Waterman, K. S. Ramamurthi, P. J. La Riviere, and H. Shroff, “Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy,” Optica 3(8), 897–910 (2016).
[Crossref] [PubMed]

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Xie, W.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

Yin, C.

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

York, A. G.

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Yoshida, K.

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

Yu, T.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

Yuste, R.

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Zhang, H.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Zhao, H.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Zhemkov, V.

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

Zhu, D.

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[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]

Adv. Photonics (1)

P. Fei, J. Nie, J. Lee, Y. Ding, S. Li, H. Zhang, M. Hagiwara, T. Yu, T. Segura, C.-M. Ho, D. Zhu, and T. K. Hsiai, “Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens,” Adv. Photonics 1(01), 1 (2019).
[Crossref]

Arch. Pathol. Lab. Med. (1)

A. H. Boag, L. A. Kennedy, and M. J. Miller, “Three-dimensional Microscopic Image Reconstruction of Prostatic Adenocarcinoma,” Arch. Pathol. Lab. Med. 125(4), 562–566 (2001).
[PubMed]

Bioinformatics (1)

S. Preibisch, S. Saalfeld, and P. Tomancak, “Globally optimal stitching of tiled 3D microscopic image acquisitions,” Bioinformatics 25(11), 1463–1465 (2009).
[Crossref] [PubMed]

Biol. Bull. (1)

A. Kumar, R. Christensen, M. Guo, P. Chandris, W. Duncan, Y. Wu, A. Santella, M. Moyle, P. W. Winter, D. Colón-ramos, Z. Bao, and H. Shroff, “Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM),” Biol. Bull. 231(1), 26–39 (2016).

Biomed. Opt. Express (2)

Biophys. J. (1)

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref] [PubMed]

BMC Biol. (1)

B. Migliori, M. S. Datta, C. Dupre, M. C. Apak, S. Asano, R. Gao, E. S. Boyden, O. Hermanson, R. Yuste, and R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biol. 16(1), 57 (2018).
[Crossref] [PubMed]

Genome Biol. (1)

A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini, “CellProfiler: image analysis software for identifying and quantifying cell phenotypes,” Genome Biol. 7(10), R100 (2006).
[Crossref] [PubMed]

Histopathology (2)

Y. Tolkach, S. Thomann, and G. Kristiansen, “Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity,” Histopathology 72(6), 1051–1059 (2018).
[Crossref] [PubMed]

M. E. van Royen, E. I. Verhoef, C. F. Kweldam, W. A. van Cappellen, G. J. Kremers, A. B. Houtsmuller, and G. J. L. H. van Leenders, “Three-dimensional microscopic analysis of clinical prostate specimens,” Histopathology 69(6), 985–992 (2016).
[Crossref] [PubMed]

J. Biomed. Opt. (3)

D. S. Gareau, Y. Li, B. Huang, Z. Eastman, K. S. Nehal, and M. Rajadhyaksha, “Confocal mosaicing microscopy in Mohs skin excisions: feasibility of rapid surgical pathology,” J. Biomed. Opt. 13(5), 054001 (2008).
[Crossref] [PubMed]

W. Xie, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, J. T. C. Liu, W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A. K. Glaser, M. E. Fauver, E. J. Seibel, S. M. Dintzis, J. C. Vaughan, N. P. Reder, and J. T. C. Liu, “Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins,” J. Biomed. Opt. 24(2), 026501 (2019)

P. Kennel, L. Teyssedre, J. Colombelli, and F. Plouraboué, “Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy,” J. Biomed. Opt. 23(8), 1–14 (2018).
[Crossref] [PubMed]

J. Innov. Opt. Health Sci. (1)

S. Liu, T. Yu, P. Fei, D. Zhu, J. Nie, and Y. Li, “Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy,” J. Innov. Opt. Health Sci. 10(05), 1743006 (2017).
[Crossref]

Microsc. Microanal. (1)

R. Levenson, F. Fereidouni, Z. Harmany, M. Tan, M. Lechpammer, and S. Demos, “Slide-Free Microscopy via UV Surface Excitation,” Microsc. Microanal. 22(S3), 1002–1003 (2016).
[Crossref]

Nat. Biomed. Eng. (1)

A. K. Glaser, N. P. Reder, Y. Chen, E. F. McCarty, C. Yin, L. Wei, Y. Wang, L. D. True, and J. T. C. Liu, “Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens,” Nat. Biomed. Eng. 1(7), 0084 (2017).
[Crossref] [PubMed]

Nat. Biotechnol. (1)

Y. Wu, P. Wawrzusin, J. Senseney, R. S. Fischer, R. Christensen, A. Santella, A. G. York, P. W. Winter, C. M. Waterman, Z. Bao, D. A. Colón-Ramos, M. McAuliffe, and H. Shroff, “Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy,” Nat. Biotechnol. 31(11), 1032–1038 (2013).
[Crossref] [PubMed]

Nat. Methods (8)

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]

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

P. J. Keller, M. B. Ahrens, and J. Freeman, “Light-sheet imaging for systems neuroscience,” Nat. Methods 12(1), 27–29 (2015).
[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]

R. M. Power and J. Huisken, “A guide to light-sheet fluorescence microscopy for multiscale imaging,” Nat. Methods 14(4), 360–373 (2017).
[Crossref] [PubMed]

R. K. Chhetri, F. Amat, Y. Wan, B. Höckendorf, W. C. Lemon, and P. J. Keller, “Whole-animal functional and developmental imaging with isotropic spatial resolution,” Nat. Methods 12(12), 1171–1178 (2015).
[Crossref] [PubMed]

S. Preibisch, S. Saalfeld, J. Schindelin, and P. Tomancak, “Software for bead-based registration of selective plane illumination microscopy data,” Nat. Methods 7(6), 418–419 (2010).
[Crossref] [PubMed]

S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, and P. Tomancak, “Efficient Bayesian-based multiview deconvolution,” Nat. Methods 11(6), 645–648 (2014).
[Crossref] [PubMed]

Nat. Protoc. (1)

A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D. A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, “Dual-view plane illumination microscopy for rapid and spatially isotropic imaging,” Nat. Protoc. 9(11), 2555–2573 (2014).
[Crossref] [PubMed]

Opt. Express (1)

Optica (1)

Pattern Recognit. (1)

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, F. W. Patten, E. J. Seibel, and A. C. Nelson, “Automated cell analysis in 2D and 3D: A comparative study,” Pattern Recognit. 42(1), 141–146 (2009).
[Crossref]

PLoS One (2)

K. N. Elfer, A. B. Sholl, M. Wang, D. B. Tulman, S. H. Mandava, B. R. Lee, and J. Q. Brown, “DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues,” PLoS One 11(10), e0165530 (2016).
[Crossref] [PubMed]

M. G. Giacomelli, L. Husvogt, H. Vardeh, B. E. Faulkner-Jones, J. Hornegger, J. L. Connolly, and J. G. Fujimoto, “Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging,” PLoS One 11(8), e0159337 (2016).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (1)

Y. K. Tao, D. Shen, Y. Sheikine, O. O. Ahsen, H. H. Wang, D. B. Schmolze, N. B. Johnson, J. S. Brooker, A. E. Cable, J. L. Connolly, and J. G. Fujimoto, “Assessment of breast pathologies using nonlinear microscopy,” Proc. Natl. Acad. Sci. U.S.A. 111(43), 15304–15309 (2014).
[Crossref] [PubMed]

Sci. Rep. (3)

M. Wang, D. B. Tulman, A. B. Sholl, H. Z. Kimbrell, S. H. Mandava, K. N. Elfer, S. Luethy, M. M. Maddox, W. Lai, B. R. Lee, and J. Q. Brown, “Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy,” Sci. Rep. 6(May), 27419 (2016).
[Crossref] [PubMed]

S. Nojima, E. A. Susaki, K. Yoshida, H. Takemoto, N. Tsujimura, S. Iijima, K. Takachi, Y. Nakahara, S. Tahara, K. Ohshima, M. Kurashige, Y. Hori, N. Wada, J. I. Ikeda, A. Kumanogoh, E. Morii, and H. R. Ueda, “CUBIC pathology: Three-dimensional imaging for pathological diagnosis,” Sci. Rep. 7(1), 9269 (2017).
[Crossref] [PubMed]

P. Lawson, A. B. Sholl, J. Q. Brown, B. T. Fasy, and C. Wenk, “Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology,” Sci. Rep. 9(1), 1139 (2019).
[Crossref] [PubMed]

Science (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Technol. Cancer Res. Treat. (1)

O. Assayag, M. Antoine, B. Sigal-Zafrani, M. Riben, F. Harms, A. Burcheri, K. Grieve, E. Dalimier, B. Le Conte de Poly, and C. Boccara, “Large Field, High Resolution Full-Field Optical Coherence Tomography: A Pre-clinical Study of Human Breast Tissue and Cancer Assessment,” Technol. Cancer Res. Treat. 13(5), 455–468 (2014).
[PubMed]

Other (2)

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues,” bioRxiv Prepr. 1–16 (2019).

T. Chakraborty, M. Driscoll, M. Murphy, P. Roudot, B.-J. Chang, S. Vora, W. M. Wong, C. Nielson, H. Zhang, V. Zhemkov, C. Hiremath, E. D. D. La Cruz, I. Bezprozvanny, H. Zhao, R. Tomer, R. Heintzmann, J. Meeks, D. Marciano, S. Morrison, G. Danuser, K. M. Dean, and R. Fiolka, “Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging,” bioRxiv (preprint).

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Figures (7)

Fig. 1
Fig. 1 diSPIM schematic. A virtual light sheet generated by one of the micro-mirror scanners that scans in the y(y') direction rapidly illuminates the sample through the illumination objective at an oblique 45° angle from one objective. The emission signal from the sample is then collected by the detection objective lens positioned perpendicular to the illumination objective and imaged with the dedicated camera for that side. The stage moves in the x direction to create a 3D stack. The objectives move vertically to achieve extended z depth (A). The two light paths can then switch roles for illumination and detection alternatively for dual-view imaging. Compared to the traditional xyz coordinates, a new set of coordinates of x'A/By'z'A/B for diSPIM is used. X'A/B axis is along the illumination direction of left/right light path, z'A/B is the corresponding detection axis of view A/B (B), and y' is the same as y (C). BS: beam splitter. MM: micro-mirror scanner. TL: adjustable tube lens. DM + F: dichroic mirror + emission filter. Ill obj: illumination objective. Det obj: detection objective.
Fig. 2
Fig. 2 Comparison of PSFs in x'y', x'z' and y'z' views, between one of the single-views and the dual-view deconvolution results, of 500 nm fluorescent beads phantom. All of the images are maximum intensity projections of shifted x'y' stacks along the z' axis. The bottom Gaussian fitted intensity plots are along x', z' and y' directions from left to right, based on the beads indicated with blue solid lines in single-views and red dash lines in dual-view deconvolved results. All scale bars denote 10 μm.
Fig. 3
Fig. 3 Deconvoluted volume of D&E stained buccal cells sample (A) and the minimum intensity projections comparisons in three views between single-view and deconvolution results (B-J). The green arrows and blue circles in A, B and C indicate the same region of the sample. Note that rotating the data to an appropriate orientation could differentiate cells that are overlapped in 2D slices. Also, the resolution in y'z' and x'z' have been improved significantly by dual-view fusion and deconvolution (D-G, I-J). Scale bar in A: 150 μm, in B, C, H: 100 μm. Decon: Dual-view deconvolved. MIP: minimum intensity projection.
Fig. 4
Fig. 4 Dual-view deconvolved volume reconstruction (B, 11,151 × 2,002 × 355 voxels, 4.3 mm × 0.78 mm × 0.14 mm) from a large D&E-stained, cleared prostate biopsy (A, 37,955 × 6,860 × 1,100 voxels, 14.8 mm × 2.7 mm × 0.4 mm, single-view reconstruction shown), and selected ortho-sections in XY at depth of about 65 μm (C), XZ (D) and YZ (E). The locations of the ortho-sections in the sample are indicated with the orange, blue and green boxes in B. The border colors in C-E match the color of the boxes in B. Zoomed-in XY ortho-slices (location indicated by the black box in C) at different depths are also shown in F. Scale bar in A: 2 mm, B-D: 500 μm, E: 200 μm, and F: 100 μm.
Fig. 5
Fig. 5 Small areas in XY, XZ and YZ planes from SPIM-A, SPIM-B and dual-view deconvolved (Decon) prostate data sets were chosen to compare high resolution local image details. Each image was a minimum intensity projection of 11 sequential images to avoid z offset among SPIM-A, SPIM-B and Decon views. Inverted intensity profiles were plotted among the same locations in SPIM-A, SPIM-B and Decon, indicated by lines in the SPIM-A image column. Scale bar: 15 μm.
Fig. 6
Fig. 6 Cell nuclei counts in the same volume from SPIM-A, SPIM-B, and Decon voumes, and from the approximate same volume from H&E slides. Decon has significant more cell number than the two single-view results and has a closer cell number to H&E images.
Fig. 7
Fig. 7 Normalized X, Y and Z projections in frequency domain, with higher frequency bandwidth in dual-view deconvolved prostate images (Decon-A + B) versus SPIM-A, SPIM-B, or SPIM-A deconvolved (Decon-A) data sets. The inset in A shows a zoomed-in area in the plots, indicating removal of high-frequency striping artifacts by dual-view deconvolution.

Tables (1)

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Table 1 Integration of Normalized X, Y and Z projection in frequency domain