Optical sectioning methods in three-dimensional bioimaging

Jing Zhang; Wei Qiao; Rui Jin; Hongjin Li; Hui Gong; Shih-Chi Chen; Qingming Luo; Jing Yuan

doi:10.1038/s41377-024-01677-x

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Optical sectioning methods in three-dimensional bioimaging

Review

- Optical sectioning methods in three-dimensional bioimaging
- Optical sectioning methods in three-dimensional bioimaging
- LSA 2025年14卷第1期页码：47-74
- Affiliations：
  
  1.Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
  2.MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China
  3.Hong Kong Center for Cerebro-Cardiovascular Health Engineering, N.T, Hong Kong, China
  4.Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
  5.HUST-Suzhou Institute for Brainsmatics, Suzhou, China
  6.Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
  7.School of Biomedical Engineering, Hainan University, Haikou, China
- Author bio：
  
  Shih-Chi Chen (scchen@mae.cuhk.edu.hk)
  Qingming Luo (qluo@hainanu.edu.cn)
  Jing Yuan (yuanj@hust.edu.cn)
- Funds：
- DOI：10.1038/s41377-024-01677-x
  中图分类号：
- 纸质出版日期：2025-01-31，
  
  网络出版日期：2025-01-01，
  
  收稿日期：2024-05-11，
  
  修回日期：2024-09-24，
  
  录用日期：2024-10-28
- Accepted：
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Optical sectioning methods in three-dimensional bioimaging[J]. LSA, 2025,14(1):47-74.

Zhang, J. et al. Optical sectioning methods in three-dimensional bioimaging. Light: Science & Applications, 14, 47-74 (2025).
Optical sectioning methods in three-dimensional bioimaging[J]. LSA, 2025,14(1):47-74. DOI： 10.1038/s41377-024-01677-x.

Zhang, J. et al. Optical sectioning methods in three-dimensional bioimaging. Light: Science & Applications, 14, 47-74 (2025). DOI： 10.1038/s41377-024-01677-x.

摘要

Abstract

In recent advancements in life sciences

optical microscopy has played a crucial role in acquiring high-quality three-dimensional structural and functional information. However

the quality of 3D images is often compromised due to the intense scattering effect in biological tissues

compounded by several issues such as limited spatiotemporal resolution

low signal-to-noise ratio

inadequate depth of penetration

and high phototoxicity. Although various optical sectioning techniques have been developed to address these challenges

each method adheres to distinct imaging principles for specific applications. As a result

the effective selection of suitable optical sectioning techniques across diverse imaging scenarios has become crucial yet challenging. This paper comprehensively overviews existing optical sectioning techniques and selection guidance under different imaging scenarios. Specifically

we categorize the microscope design based on the spatial relationship between the illumination and detection axis

i.e.

on-axis and off-axis. This classification provides a unique perspective to compare the implementation and performances of various optical sectioning approaches. Lastly

we integrate selected optical sectioning methods on a custom-built off-axis imaging system and present a unique perspective for the future development of optical sectioning techniques.

关键词

Keywords

references

Pawley, J. B. Handbook of Biological Confocal Microscopy. 3rd edn. (New York: Springer, 2006).

So, P. T. C. et al. Two-photon excitation fluorescence microscopy. Annu Rev. Biomed. Eng. 2 , 399–429 (2000)..

Im, K. B. et al. Simple high-speed confocal line-scanning microscope. Opt. Express 13 , 5151–5156 (2005)..

Tanaami, T. et al. High-speed 1-frame/ms scanning confocal microscope with a microlens and Nipkow disks. Appl Opt. 41 , 4704–4708 (2002)..

Neil, M. A. A., Juškaitis, R. & Wilson, T. Method of obtaining optical sectioning by using structured light in a conventional microscope. Opt. Lett. 22 , 1905–1907 (1997)..

Huisken, J. et al. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305 , 1007–1009 (2004)..

Zhong, Q. Y. et al. High-definition imaging using line-illumination modulation microscopy. Nat. Methods 18 , 309–315 (2021)..

Wilson, T. Optical sectioning in confocal fluorescent microscopes. J. Microsc 154 , 143–156 (1989)..

Sheppard, C. J. R. & Mao, X. Q. Confocal microscopes with slit apertures. J. Mod. Opt. 35 , 1169–1185 (1988)..

Wilson, T. & Carlini, A. R. Size of the detector in confocal imaging systems. Opt. Lett. 12 , 227–229 (1987)..

Wilson, T. Resolution and optical sectioning in the confocal microscope. J. Microsc 244 , 113–121 (2011)..

Dan, D., Yao, B. L. & Lei, M. Structured illumination microscopy for super-resolution and optical sectioning. Chin. Sci. Bull. 59 , 1291–1307 (2014)..

Lim, D. et al. Optically sectioned in vivo imaging with speckle illumination HiLo microscopy. J. Biomed. Opt. 16 , 016014 (2011)..

Poher, V. et al. Improved sectioning in a slit scanning confocal microscope. Opt. Lett. 33 , 1813–1815 (2008)..

Liu, C. G. et al. In vivo super-resolution retinal imaging through virtually structured detection. J. Biomed. Opt. 21 , 120502 (2016)..

Zhong, Q. Y. et al. High-throughput optical sectioning via line-scanning imaging with digital structured modulation. Opt. Lett. 46 , 504–507 (2021)..

Qiao, W. et al. Single-scan HiLo with line-illumination strategy for optical section imaging of thick tissues. Biomed. Opt. Express 12 , 2373–2383 (2021)..

Minsky, M. Memoir on inventing the confocal scanning microscope. Scanning 10 , 128–138 (1988)..

Brakenhoff, G. J. et al. Three-dimensional confocal fluorescence microscopy. Methods Cell Biol. 30 , 379–398 (1989)..

Lichtman, J. W., Sunderland, W. J. & Wilkinson, R. S. High-resolution imaging of synaptic structure with a simple confocal microscope. N. Biologist 1 , 75–82 (1989)..

Choi, S. et al. Development of a high speed laser scanning confocal microscope with an acquisition rate up to 200 frames per second. Opt. Express 21 , 23611–23618 (2013)..

Jonkman, J. et al. Tutorial: guidance for quantitative confocal microscopy. Nat. Protoc. 15 , 1585–1611 (2020)..

Jesacher, A., Bernet, S. & Ritsch-Marte, M. Colored point spread function engineering for parallel confocal microscopy. Opt. Express 24 , 27395–27402 (2016)..

Wolleschensky, R., Zimmermann, B. & Kempe, M. High-speed confocal fluorescence imaging with a novel line scanning microscope. J. Biomed. Opt. 11 , 064011 (2006)..

Martin, C. et al. Line excitation array detection fluorescence microscopy at 0.8 million frames per second. Nat. Commun. 9 , 4499 (2018)..

Chang, S. T. & Xia, H. J. Flat-field correction for high-throughput fluorescence microscopy. Optical Eng. 61 , 034107 (2022)..

Conchello, J. A. & Lichtman, J. W. Optical sectioning microscopy. Nat. Methods 2 , 920–931 (2005)..

Gräf, R., Rietdorf, J.&Zimmermann, T. Live cell spinning disk microscopy. in Microscopy Techniques (ed Rietdorf, J.) (Berlin: Springer, 2005), 57-75.

Shimozawa, T. et al. Improving spinning disk confocal microscopy by preventing pinhole cross-talk for intravital imaging. Proc. Natl Acad. Sci. USA 110 , 3399–3404 (2013)..

Li, X. et al. Fast confocal microscopy imaging based on deep learning. Proceedings of the IEEE International Conference on Computational Photography. St. Louis, MO, USA: IEEE, 2020, 1-12.

Chen, X. et al. Artificial confocal microscopy for deep label-free imaging. Nat. Photonics 17 , 250–258 (2023)..

Fang, L. J. et al. Deep learning-based point-scanning super-resolution imaging. Nat. Methods 18 , 406–416 (2021)..

Tsang, J. M. et al. Fast, multiplane line-scan confocal microscopy using axially distributed slits. Biomed. Opt. Express 12 , 1339–1350 (2021)..

Wu, Y. C. et al. Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning. Nat. Methods 16 , 1323–1331 (2019)..

Hell, S. W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19 , 780–782 (1994)..

Fölling, J. et al. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat. Methods 5 , 943–945 (2008)..

Nägerl, U. V. et al. Live-cell imaging of dendritic spines by STED microscopy. Proc. Natl Acad. Sci. USA 105 , 18982–18987 (2008)..

Lee, W. S. et al. Investigation on improvement of lateral resolution of continuous wave STED microscopy by standing wave illumination. Opt. Express 26 , 9901–9919 (2018)..

Vicidomini, G., Bianchini, P. & Diaspro, A. STED super-resolved microscopy. Nat. Methods 15 , 173–182 (2018)..

Heine, J. et al. Adaptive-illumination STED nanoscopy. Proc. Natl Acad. Sci. USA 114 , 9797–9802 (2017)..

Huang, B. Y. et al. Correction: enhancing image resolution of confocal fluorescence microscopy with dee p learning. PhotoniX 4 , 5 (2023)..

De Luca, G. M. R. et al. Re-scan confocal microscopy: scanning twice for better resolution. Biomed. Opt. Express 4 , 2644–2656 (2013)..

Müller, C. B. & Enderlein, J. Image scanning microscopy. Phys. Rev. Lett. 104 , 198101 (2010)..

Roth, S. et al. Optical photon reassignment microscopy (OPRA). Optical Nanoscopy 2 , 5 (2013)..

Sheppard, C. J. R., Mehta, S. B. & Heintzmann, R. Superresolution by image scanning microscopy using pixel reassignment. Opt. Lett. 38 , 2889–2892 (2013)..

Sibarita, J. B. Deconvolution microscopy. in Microscopy Techniques (ed Rietdorf, J.) (Berlin: Springer, 2005), 201-243.

Guo, M. et al. Rapid image deconvolution and multiview fusion for optical microscopy. Nat. Biotechnol. 38 , 1337–1346 (2020)..

Zhao, W. S. et al. Sparse deconvolution improves the resolution of live-cell super-res olution fluorescence microscopy. Nat. Biotechnol. 40 , 606–617 (2022)..

Li, H. J. et al. Pixel-reassigned line-scanning microscopy for fast volumetric super-resolution imaging. Opt. Express 32 , 2347–2355 (2024)..

Huff, J. The Airyscan detector from ZEISS: confocal imaging with improved signal-to-noise ratio and super-resolution. Nat Methods 12, ⅰ–ⅱ (2015).

Kuang, C. F. et al. Breaking the diffraction barrier using fluorescence emission difference microscopy. Sci. Rep. 3 , 1441 (2013)..

Li, C. K. et al. Resolution enhancement and background suppression in optical super-resolution imaging for biological applications. Laser Photonics Rev. 15 , 1900084 (2021)..

Oheim, M. et al. Principles of two-photon excitation fluorescence microscopy and other nonlinear imaging approaches. Adv. Drug Deliv. Rev. 58 , 788–808 (2006)..

Svoboda, K. & Yasuda, R. Principles of two-photon excitation microscopy and its applications to neuroscience. Neuron 50 , 823–839 (2006)..

Katona, G. et al. Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes. Nat. Methods 9 , 201–208 (2012)..

Nadella, K. M. N. S. et al. Random-access scanning microscopy for 3D imaging in awake behaving animals. Nat. Methods 13 , 1001–1004 (2016)..

Geng, Q. et al. Digital micromirror device-based two-photon microscopy for three-dimensional and random-access imaging. Optica 4 , 674–677 (2017)..

Tsai, P. S. et al. Ultra-large field-of-view two-photon microscopy. Opt. Express 23 , 13833–13847 (2015)..

Bewersdorf, J., Pick, R. & Hell, S. W. Multifocal multiphoton microscopy. Opt. Lett. 23 , 655–657 (1998)..

Ströhl, F. et al. Multifocus microscopy with optical sectioning and high axial resolution. Optica 9 , 1210–1218 (2022)..

Villette, V. et al. Ultrafast two-photon imaging of a high-gain voltage indicator in awake beh aving mice. Cell 179 , 1590–1608.e23 (2019)..

Zhang, T. et al. Kilohertz two-photon brain imaging in awake mice. Nat. Methods 16 , 1119–1122 (2019)..

Wu, J. L. et al. Kilohertz two-photon fluorescence microscopy imaging of neural activity in vivo. Nat. Methods 17 , 287–290 (2020)..

Li, R. J. et al. Ten-kilohertz two-photon microscopy imaging of single-cell dendritic activity and hemodynamics in vivo. Neurophotonics 10 , 025006 (2023)..

Wen, C. Y. et al. Compressive sensing for fast 3-D and random-access two-photon microscopy. Opt. Lett. 44 , 4343–4346 (2019)..

Wu, J. L., Ji, N. & Tsia, K. K. Speed scaling in multiphoton fluorescence microscopy. Nat. Photonics 15 , 800–812 (2021)..

Wu, J. L. et al. Ultrafast laser-scanning time-stretch imaging at visible wavelengths. Light Sci. Appl 6 , e16196 (2017)..

Papagiakoumou, E., Ronzitti, E. & Emiliani, V. Scanless two-photon excitation with temporal focusing. Nat. Methods 17 , 571–581 (2020)..

Xue, Y. et al. Scattering reduction by structured light illumination in line-scanning temporal focusing microscopy. Biomed. Opt. Express 9 , 5654–5666 (2018)..

Shi, R. H. et al. HiLo based line scanning temporal focusing microscopy for high-speed, deep tissue imaging. Membranes 11 , 634 (2021)..

Helmchen, F. & Denk, W. Deep tissue two-photon microscopy. Nat. Methods 2 , 932–940 (2005)..

Ingaramo, M. et al. Two-photon excitation improves multifocal structured illumination microscopy in thick scattering tissue. Proc. Natl Acad. Sci. USA 111 , 5254–5259 (2014)..

Choi, H. et al. Improvement of axial resolution and contrast in temporally focused widefield two-photon microscopy with structured light illumination. Biomed. Opt. Express 4 , 995–1005 (2013)..

Takanezawa, S., Saitou, T. & Imamura, T. Wide field light-sheet microscopy with lens-axicon controlled two-photon be ssel beam illumination. Nat. Commun. 12 , 2979 (2021)..

Meng, Y. L. et al. Fast two-snapshot structured illumination for temporal focusing microscopy with enhanced axial resolution. Opt. Express 25 , 23109–23121 (2017)..

Axelrod, D. Total internal reflection fluorescence microscopy. Methods Cell Biol. 30 , 245–270, https://doi.org/10.1016/S0091-679X(08)60982-6 (1989)..

Axelrod, D. Total internal reflection fluorescence microscopy in cell biology. Traffic 2 , 764–774 (2001)..

Steyer, J. A. & Almers, W. A real-time view of life within 100 nm of the plasma membrane. Nat. Rev. Mol. Cell Biol. 2 , 268–275 (2001)..

Mattheyses, A. L., Simon, S. M. & Rappoport, J. Z. Imaging with total internal reflection fluorescence microscopy for the cell biologist. J. Cell Sci. 123 , 3621–3628 (2010)..

Guo, Y. T. et al. Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales. Cell 175 , 1430–1442.e17 (2018)..

Bozinovic, N. et al. Fluorescence endomicroscopy with structured illumination. Opt. Express 16 , 8016–8025 (2008)..

Mertz, J. Optical sectioning microscopy with planar or structured illumination. Nat. Methods 8 , 811–819 (2011)..

Supekar, O. D. et al. Miniature structured illumination microscope for in vivo 3D imaging of brain structures with optical sectioning. Biomed. Opt. Express 13 , 2530–2541 (2022)..

Dan, D. et al. DMD-based LED-illumination super-resolution and optical sectioning microscopy. Sci. Rep. 3 , 1116 (2013)..

Xu, D. L. et al. Fast optical sectioning obtained by structured illumination microscopy using a digital mirror device. J. Biomed. Opt. 18 , 060503 (2013)..

Fu, Z. Q. et al. Single-shot optical sectioning microscopy based on structured illumination. Opt. Lett. 47 , 814–817 (2022)..

Chen, J. L. et al. Holography-based structur ed light illumination for temporal focusing microscopy. Opt. Lett. 46 , 3143–3146 (2021)..

Gustafsson, M. G. L. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc 198 , 82–87 (2000)..

Wu, Y. C. & Shroff, H. Faster, sharper, and deeper: structured illumination microscopy for biological imaging. Nat. Methods 15 , 1011–1019 (2018)..

Ma, Y. et al. Recent advances in structured illumination microscopy. J. Phys: Photonics 3 , 024009 (2021)..

Chen, X. et al. Superresolution structured illumination microscopy reconstruction algorithms: a review. Light Sci. Appl 12 , 172 (2023)..

Langhorst, M. F., Schaffer, J. & Goetze, B. Structure brings clarity: structured illumination microscopy in cell biology. Biotechnol. J. 4 , 858–865 (2009)..

Ströhl, F. & Kaminski, C. F. Frontiers in structured illumination microscopy. Optica 3 , 667–677 (2016)..

Wen, G. et al. High-fidelity structured illumination microscopy by point-spread-function engineering. Light Sci. Appl 10 , 70 (2021)..

Young, L. J., Ströhl, F. & Kaminski, C. F. A guide to structured illumination TIRF microscopy at high speed with multiple colors. J. Visualized Exp. 111 , e53988, https://doi.org/10.3791/53988 (2016)..

Liu, W. J. et al. Three-dimensional super-resolution imaging of live whole cells using galvanometer-based structured illumination microscopy. Opt. Express 27 , 7237–7248 (2019)..

Li, X. S. et al. Three-dimensional structured illumination microscopy with enhanced axial resolution. Nat. Biotechnol. 41 , 1307–1319 (2023)..

Gustafsson, M. G. L. et al. Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophysical J. 94 , 4957–4970 (2008)..

Laporte, G. P. J. et al. Resolution enhancement in nonlinear scanning microscopy through post-detection digital computation. Optica 1 , 455–460 (2014)..

Kuang, C. F. et al. Virtual k -space modulation optical microscopy. Phys. Rev. Lett. 117 , 028102 (2016)..

Urban, B. E. et al. Super-resolution two-photon microscopy via scanning patterned illumination. Phys. Rev. E 91 , 042703 (2015)..

Yeh, C. H. & Chen, S. Y. Resolution enhancement of two-photon microscopy via intensity-modulated laser scanning structured illumination. Appl Opt. 54 , 2309–2317 (2015)..

Mandula, O. et al. Line scan-structured illumination microscopy super-resolution imaging in thick fluorescent samples. Opt. Express 20 , 24167–24174 (2012)..

Li, Z. W. et al. Contrast and resolution enhanced optical sectioning in scattering tissue using line-scanning two-photon structured illumination microscopy. Opt. Express 25 , 32010–32020 (2017)..

Zhang, X. Y. et al. Deep learning optical-sectioning method. Opt. Express 26 , 30762–30772 (2018)..

Jin, L. H. et al. Deep learning enables struc tured illumination microscopy with low light levels and enhanced speed. Nat. Commun. 11 , 1934 (2020)..

Krzewina, L. G. & Kim, M. K. Single-exposure optical sectioning by color structured illumination microscopy. Opt. Lett. 31 , 477–479 (2006)..

Wicker, K. & Heintzmann, R. Single-shot optical sectioning using polarization-coded structured illumination. J. Opt. 12 , 084010 (2010)..

Ventalon, C. & Mertz, J. Dynamic speckle illumination microscopy with translated versus randomized speckle patterns. Opt. Express 14 , 7198–7209 (2006)..

Ventalon, C., Heintzmann, R. & Mertz, J. Dynamic speckle illumination microscopy with wavelet prefiltering. Opt. Lett. 32 , 1417–1419 (2007)..

Lim, D., Chu, K. K. & Mertz, J. Wide-field fluorescence sectioning with hybrid speckle and uniform-illumination microscopy. Opt. Lett. 33 , 1819–1821 (2008)..

Santos, S. et al. Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle. J. Biomed. Opt. 14 , 030502 (2009)..

Jiang, S. H. & Walker, J. G. Speckle-illuminated fluorescence confocal microscopy, using a digital micro-mirror device. Meas. Sci. Technol. 20 , 065501 (2009)..

Choi, Y. et al. Full-field and single-shot quantitative phase microscopy using dynamic speckle illumination. Opt. Lett. 36 , 2465–2467 (2011)..

Ford, T. N., Lim, D. & Mertz, J. Fast optically sectioned fluorescence HiLo endomicroscopy. J. Biomed. Opt. 17 , 021105 (2012)..

Zhang, H. J., Vyas, K. & Yang, G. Z. Line scanning, fiber bundle fluorescence HiLo endomicroscopy with confocal slit detection. J. Biomed. Opt. 24 , 116501 (2019)..

Keller, P. J. et al. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322 , 1065–1069 (2008)..

Santi, P. A. Light sheet fluorescence microscopy: a review. J. Histochemistry Cytochemistry 59 , 129–138 (2011)..

Keller, P. J. et al. Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy. Nat. Methods 7 , 637–642 (2010)..

Mertz, J. & Kim, J. Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection. J. Biomed. Opt. 15 , 016027 (2010)..

Schacht, P., Johnson, S. B. & Santi, P. A. Implementation of a continuous scanning procedure and a line scan camera for thin-sheet laser imaging microscopy. Biomed. Opt. Express 1 ,598–609 (2010)..

Baumgart, E. & Kubitscheck, U. Scanned light sheet microscopy with confocal slit detection. Opt. Express 20 , 21805–21814 (2012)..

Luna-Palacios, Y. Y. et al. Multicolor light-sheet microscopy for a large field of view imaging: a comparative study between bessel and gaussian light-sheets configurations. J. Biophotonics 15 , e202100359 (2022)..

Olarte, O. E. et al. Image formation by linear and nonlinear digital scanned light-sheet fluorescence microscopy with gaussian and bessel beam profiles. Biomed. Opt. Express 3 , 1492–1505 (2012)..

Tomer, R. et al. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat. Methods 9 , 755–763 (2012)..

Dodt, H. U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4 , 331–336 (2007)..

Becker, K. et al. Ultramicroscopy: 3D reconstruction of large microscopical specimens. J. Biophotonics 1 , 36–42 (2008)..

Krzic, U. et al. Multiview light-sheet microscope for rapid in toto imaging. Nat. Methods 9 , 730–733 (2012)..

Kim, B. et al. Open-top axially swept light-sheet microscopy. Biomed. Opt. Express 12 , 2328–2338 (2021)..

Fahrbach, F. O., Simon, P. & Rohrbach, A. Microscopy with self-reconstructing beams. Nat. Photonics 4 , 780–785 (2010)..

Fahrbach, F. O. et al. Light-sheet microscopy in thic k media using scanned bessel beams and two-photon fluorescence excitation. Opt. Express 21 , 13824–13839 (2013)..

Fahrbach, F. O. et al. Self-reconstructing sectioned bessel beams offer submicron optical sectioning for large fields of view in light-sheet microscopy. Opt. Express 21 , 11425–11440 (2013)..

Vettenburg, T. et al. Light-sheet microscopy using an airy beam. Nat. Methods 11 , 541–544 (2014)..

Hosny, N. A. et al. Planar airy beam light-sheet for two-photon microscopy. Biomed. Opt. Express 11 , 3927–3935 (2020)..

Dunsby, C. Optically sectioned imaging by oblique plane microscopy. Opt. Express 16 , 20306–20316 (2008)..

Wu, Y. C. et al. Inverted selective plane illumination microscopy ( i SPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 108 , 17708–17713 (2011)..

Cutrale, F. & Gratton, E. Inclined selective plane illumination microscopy adaptor for conventional microscopes. Microsc Res Tech. 75 , 1461–1466 (2012)..

Gao, L. Extend the field of view of selective plan illumination microscopy by tiling the excitation light sheet. Opt. Express 23 , 6102–6111 (2015)..

Strnad, P. et al. Inverted light-sheet microscope for imaging mouse pre-implantation development. Nat. Methods 13 , 139–142 (2016)..

Sapoznik, E. et al. A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. eLife 9 , e57681 (2020)..

Chakraborty, T. et al. Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution. Nat. Methods 16 , 1109–1113 (2019)..

Zhao, Y. X. et al. Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales. Nat. Methods 19 , 359–369 (2022)..

Voigt, F. F. et al. The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nat. Methods 16 , 1105–1108 (2019)..

Chen, Y. L. et al. A versatile tiling light sheet microscope for imaging of cleared tissues. Cell Rep. 33 , 108349 (2020)..

Glaser, A. K. et al. A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues. Nat. Methods 19 , 613–619 (2022)..

Power, R. M. & Huisken, J. A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat. Methods 14 , 360–373 (2017)..

Hillman, E. M. C. et al. Light-sheet microscopy in neuroscience. Annu Rev. Neurosci. 42 , 295–313 (2019)..

Bouchard, M. B. et al. Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms. Nat. Photonics 9 , 113–119 (2015)..

Meddens, M. B. M. et al. Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution. Biomed. Opt. Express 7 , 2219–2236 (2016)..

Kumar, M. et al. Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging. Opt. Express 26 , 13027–13041 (2018)..

Kumar, M. & Kozorovitskiy, Y. Tilt-invariant scanned oblique plane illumination microscopy for large-scale volumetric imaging. Opt. Lett. 44 , 1706–1709 (2019)..

Voleti, V. et al. Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0. Nat. Methods 16 , 1054–1062 (2019)..

Yang, B. et al. DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy. Nat. Methods 19 , 461–469 (2022)..

Jiao, Z. F. et al. Simultaneous multi-plane imaging light-sheet fluorescence microscopy for simultaneously acquiring neuronal activity at varying depths. Optica 10 , 239–247 (2023)..

Fang, C. Y. et al. Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy. Nat. Commun. 12 , 107 (2021)..

Zhao, F. et al. Deep-learning super-resolution light-sheet add-on microscopy (Deep-SLAM) for easy isotropic volumetric imaging of large biological specimens. Biomed. Opt. Express 11 , 7273–7285 (2020)..

Chen, B. C. et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346 , 1257998 (2014)..

Gao, L. et al. Lattice light sheet microscopy using tiling lattice light sheets. Opt. Express 27 , 1497–1506 (2019)..

Chen, B. Y. et al. Resolution doubling in light-sheet microscopy via oblique plane structured illumination. Nat. Methods 19 , 1419–1426 (2022)..

Shi, Y., Daugird, T. A. & Legant, W. R. A quantitative analysis of various patterns applied in lattice light sheet microscopy. Nat. Commun. 13 , 4607 (2022)..

Wang, Z. et al. Axial resolution and imaging contrast enhancement in inverted light-sheet microscopy by natural illumination modulation. Front Neurosci. 16 , 1032195 (2022)..

Qiao, W. et al. Differential synthetic i llumination based on multi-line detection for resolution and contrast enhancement of line confocal microscopy. Opt. Express 31 , 16093–16106 (2023)..

Santi, P. A. et al. Thin-sheet laser imaging microscopy for optical sectioning of thick tissues. Biotechniques 46 , 287–294 (2009)..

Li, C. et al. Illumination angle correction during image acquisition in light-sheet fluorescence microscopy using deep learning. Biomed. Opt. Express 13 , 888–901 (2022)..

Wilson, T. Spinning-disk microscopy systems. Cold Spring Harb. Protoc. 11 , 1208–1214 (2010)..

Hagen, N., Gao, L. & Tkaczyk, T. S. Quantitative sectioning and noise analysis for structured illumination microscopy. Opt. Express 20 , 403–413 (2012)..

Thomas, B., Momany, M. & Kner, P. Optical sectioning structured illumination microscopy with enhanced sensitivity. J. Opt. 15 , 094004 (2013)..

Oheim, M. et al. Two-photon microscopyin brain tissue: parameters influencing the imaging depth. J. Neurosci. Methods 111 , 29–37 (2001)..

Stock, K. et al. Variable‐angle total internal reflection fluorescence microscopy (VA‐TIRFM): realization and application of a compact illumination device. J. Microsc 211 , 19–29 (2003)..

Koester, H. J. et al. Ca 2+ fluorescence imaging with pico- and femtosecond two-photon excitation: signal and photodamage. Biophysical J. 77 , 2226–2236 (1999)..

Patterson, G. H. & Piston, D. W. Photobleaching in two-photon excitation microscopy. Biophysical J. 78 , 2159–2162 (2000)..

Hopt, A. & Neher, E. Highly nonlinear photodamage in two-photon fluorescence microscopy. Biophysical J. 80 , 2029–2036 (2001)..

Egeblad, M. et al. Visualizing stromal cell dynamics in different tumor microenvironments by spinning disk confocal microscopy. Dis. Models Mechanisms 1 , 155–167 (2008)..

Stehbens, S. et al. Imaging intracellular protein dynamics by spinning disk confocal microscopy. Methods Enzymol. 504 , 293–313 (2012)..

Dwyer, P. J., Dimarzio, C. A. & Rajadhyaksha, M. Confocal theta line-scanning microscope for imaging human tissues. Appl Opt. 46 , 1843–1851 (2007)..

Li, Y. G. et al. High-speed line-scan confocal imaging of stimulus-evoked intrinsic optical signals in the retina. Opt. Lett. 35 , 426–428 (2010)..

Vienola, K. V. et al. Parallel line scanning ophthalmoscope for retinal imaging. Opt. Lett. 40 , 5335–5338 (2015)..

Helmchen, F. et al. In vivo dendritic calcium dynamics in deep-layer cortical pyramidal neurons. Nat. Neurosci. 2 , 989–996 (1999)..

Stosiek, C. et al. In vivo two-photon calcium imaging of neuronal networks. Proc. Natl Acad. Sci. USA 100 , 7319–7324 (2003)..

Zong, W. J. et al. Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging. Nat. Methods 18 , 46–49 (2021)..

Zong, W. J. et al. Large-scale two-photon calcium imagi ng in freely moving mice. Cell 185 , 1240–1256.e30 (2022)..

Schlichenmeyer, T. C. et al. Video-rate structured illumination microscopy for high-throughput imaging of large tissue areas. Biomed. Opt. Express 5 , 366–377 (2014)..

Lauterbach, M. A. et al. Fast calcium imaging with optical sectioning via HiLo microscopy. PLoS One 10 , e0143681 (2015)..

Noël, V. P. et al. Speckled illumination HiLo microscopy for fast calcium imaging of zebrafish brain. Proceedings of the 2021 Photonics North (PN) . Toronto, ON, Canada: IEEE, 2021, 1.

Keller, P. J. & Ahrens, M. B. Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy. Neuron 85 , 462–483 (2015)..

Reynaud, E. G. et al. Guide to light-sheet microscopy for adventurous biologists. Nat. Methods 12 , 30–34 (2015)..

Farhi, S. L. et al. Wide-area all-optical neurophysiology in acute brain slices. J. Neurosci. 39 , 4889–4908 (2019)..

Qiu, S. et al. Whole-brain spatial organization of hippocampal single-neuron projectomes. Science 383 , eadj9198 (2024)..

Li, H. M. Z. et al. Single-neuron projectomes of mouse paraventricular hypothalamic nucleus oxytocin neurons reveal mutually exclusive projection patterns. Neuron 112 , 1081–1099.e7 (2024)..

BRAIN Initiative Cell Census Network (BICCN). A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 598 , 86–102 (2021)..

Ota, K. et al. Fast, cell-resolution, contiguous-wide two-photon imaging to reveal functional network architectures across multi-modal cortical areas. Neuron 109 , 1810–1824.e9 (2021)..

Huff, J. et al. Multiplex mode for the LSM 9 series with Airyscan 2: fast and gentle confocal super-resolution in large volumes. Nat. Methods 10 , 1–4, https://www.nature.com/articles/d42473-019-00173-w https://www.nature.com/articles/d42473-019-00173-w (2019)..

Jablon, K. L. et al. Isolation and short‐term culturing of primary lymphatic endothelial cells fro m collecting lymphatics: a techniques study. Microcirculation 30 , e12778 (2023)..

Lu, J. et al. Super-resolution laser scanning microscopy through spatiotemporal modulation. Nano Lett. 9 , 3883–3889 (2009)..

Panier, T. et al. Fast functional imaging of multiple brain regions in intact zebrafish larvae using selective plane illumination microscopy. Front Neural Circuits 7 , 65 (2013)..

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