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LSFM (Light Sheet Fluorescent Microscopy)

This is a list of publications on the theory, design and applications of light sheet microscopy and similar techniques. We try to keep it up-to-date, but please email Susi (spower@morgridge.org) if a paper is missing.

2014 SPIM Publications

Alvers, A. L., Ryan, S., Scherz, P. J., Huisken, J., & Bagnat, M. (2014). Single continuous lumen formation in the zebrafish gut is mediated by smoothened-dependent tissue remodeling. Development, 141(5), 1110–1119. https://doi.org/10.1242/dev.100313


Amat, F., Lemon, W., Mossing, D. P., McDole, K., Wan, Y., Branson, K., … Keller, P. J. (2014). Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nat. Methods, 11(9), 951–958. https://doi.org/10.1038/nmeth.3036


Andilla, J., Olarte, O. E., Aviles-Espinosa, R., & Loza-Alvarez, P. (2014). Imaging deep and clear in thick inhomogeneous samples. In SPIE MOEMS-MEMS (p. 89780B–89780B–7). International Society for Optics and Photonics. https://doi.org/10.1117/12.2041448


Bodea, G. O., Spille, J.-H., Abe, P., Andersson, A. S., Acker-Palmer, A., Stumm, R., … Blaess, S. (2014). Reelin and CXCL12 regulate distinct migratory behaviors during the development of the dopaminergic system. Development, 141(3), 661–673. https://doi.org/10.1242/dev.099937


Bruns, T., Schickinger, S., & Schneckenburger, H. (2014). Single plane illumination module and micro-capillary approach for a wide-field microscope. J. Vis. Exp., (90), e51993. https://doi.org/10.3791/51993


Chardès, C., Mélénec, P., Bertrand, V., & Lenne, P.-F. (2014). Setting up a simple light sheet microscope for in toto imaging of C. elegans development. J. Vis. Exp., (87). https://doi.org/10.3791/51342


Chen, B.-C., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W., … Betzig, E. (2014). Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science, 346(6208), 1257998. https://doi.org/10.1126/science.1257998


Dean, K. M., & Fiolka, R. (2014). Uniform and scalable light-sheets generated by extended focusing. Opt. Express, 22(21), 26141–26152. https://doi.org/10.1364/OE.22.026141


De Vos, W. H., Beghuin, D., Schwarz, C. J., Jones, D. B., van Loon, J. J. W. A., Bereiter-Hahn, J., & Stelzer, E. H. K. (2014). Invited review article: Advanced light microscopy for biological space research. Rev. Sci. Instrum., 85(10), 101101. https://doi.org/10.1063/1.4898123


Dobosz, M., Ntziachristos, V., Scheuer, W., & Strobel, S. (2014). Multispectral fluorescence ultramicroscopy: three-dimensional visualization and automatic quantification of tumor morphology, drug penetration, and antiangiogenic treatment response. Neoplasia, 16(1), 1–13. https://doi.org/10.1593/neo.131848


Dong, D., Arranz, A., Zhu, S., Yang, Y., Shi, L., Wang, J., … Ripoll, J. (2014). Vertically scanned laser sheet microscopy. J. Biomed. Opt., 19(10), 106001. https://doi.org/10.1117/1.JBO.19.10.106001


Eisenstein, M. (2014). Pump up the volume. Nat. Methods, 12(1), 19–22. https://doi.org/10.1038/nmeth.3220
Gao, L., Shao, L., Chen, B.-C., & Betzig, E. (2014). 3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy. Nat. Protoc., 9(5), 1083–1101. https://doi.org/10.1038/nprot.2014.087


Gao, L., Zhu, L., Li, C., & Wang, L. V. (2014). Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting. J. R. Soc. Interface, 11(93), 20130851. https://doi.org/10.1098/rsif.2013.0851


Gualda, E. J., Simão, D., Pinto, C., Alves, P. M., & Brito, C. (2014). Imaging of human differentiated 3D neural aggregates using light sheet fluorescence microscopy. Front. Cell. Neurosci., 8, 221. https://doi.org/10.3389/fncel.2014.00221


Gualda, E., Moreno, N., Tomancak, P., & Martins, G. G. (2014). Going“ open” with Mesoscopy: a new dimension on multi-view imaging. Protoplasma, 251(2), 363–372.


Höckendorf, B., Lavis, L. D., & Keller, P. J. (2014). Making biology transparent. Nat. Biotechnol., 32(11), 1104–1105. https://doi.org/10.1038/nbt.3061


Holy, T. E. (2014). Calcium imaging in populations of olfactory neurons by planar illumination microscopy. Cold Spring Harb. Protoc., 2014(3), 317–323. https://doi.org/10.1101/pdb.prot081174


Hu, Y. S., Zimmerley, M., Li, Y., Watters, R., & Cang, H. (2014). Single-molecule super-resolution light-sheet microscopy. Chemphyschem, 15(4), 577–586. https://doi.org/10.1002/cphc.201300732


Ichikawa, T., Nakazato, K., Keller, P. J., Kajiura-Kobayashi, H., Stelzer, E. H. K., Mochizuki, A., & Nonaka, S. (2014). Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools. Nat. Protoc., 9(3), 575–585. https://doi.org/10.1038/nprot.2014.035


Ingaramo, M., York, A. G., Hoogendoorn, E., Postma, M., Shroff, H., & Patterson, G. H. (2014). Richardson-Lucy deconvolution as a general tool for combining images with complementary strengths. Chemphyschem, 15(4), 794–800. https://doi.org/10.1002/cphc.201300831


Jemielita, M., Taormina, M. J., Burns, A. R., Hampton, J. S., Rolig, A. S., Guillemin, K., & Parthasarathy, R. (2014). Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut. MBio, 5(6). https://doi.org/10.1128/mBio.01751-14


Junker, J. P., Noël, E. S., Guryev, V., Peterson, K. A., Shah, G., Huisken, J., … van Oudenaarden, A. (2014). Genome-wide RNA Tomography in the zebrafish embryo. Cell, 159(3), 662–675. https://doi.org/10.1016/j.cell.2014.09.038


Ketkova, L. A., & Churbanov, M. F. (2014). 3D laser ultramicroscopy: A method for nondestructive characterization of micro- and nanoinclusions in high-purity materials for fiber and power optics. Inorg. Mater., 50(12), 1301–1316. https://doi.org/10.1134/S0020168514120097


Krieger, J. W., Singh, A. P., Garbe, C. S., Wohland, T., & Langowski, J. (2014). Dual-color fluorescence cross-correlation spectroscopy on a single plane illumination microscope (SPIM-FCCS). Opt. Express, 22(3), 2358–2375. https://doi.org/10.1364/OE.22.002358


Kumar, A., Wu, Y., Christensen, R., Chandris, P., Gandler, W., McCreedy, E., … Shroff, H. (2014). Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nat. Protoc., 9(11), 2555–2573. https://doi.org/10.1038/nprot.2014.172


Langhans, M., & Meckel, T. (2014). Single-molecule detection and tracking in plants. Protoplasma, 251(2), 277–291. https://doi.org/10.1007/s00709-013-0601-0


Lauri, A., Brunet, T., Handberg-Thorsager, M., Fischer, A. H. L., Simakov, O., Steinmetz, P. R. H., … Arendt, D. (2014). Development of the annelid axochord: insights into notochord evolution. Science, 345(6202), 1365–1368. https://doi.org/10.1126/science.1253396


Li, R., Zhou, X., Wu, D., Peng, T., Yang, Y., Lei, M., … Ye, T. (2014). Selective plane illumination microscopy with structured illumination based on spatial light modulators. In SPIE BiOS (p. 89491S–89491S–5). International Society for Optics and Photonics. https://doi.org/10.1117/12.2040319


Lim, J., Lee, H. K., Yu, W., & Ahmed, S. (2014). Light sheet fluorescence microscopy (LSFM): past, present and future. Analyst, 139(19), 4758–4768. https://doi.org/10.1039/C4AN00624K


Mahou, P., Vermot, J., Beaurepaire, E., & Supatto, W. (2014). Multicolor two-photon light-sheet microscopy. Nat. Methods, 11(6), 600–601. https://doi.org/10.1038/nmeth.2963


Maruyama, A., Oshima, Y., Kajiura-Kobayashi, H., Nonaka, S., Imamura, T., & Naruse, K. (2014). Wide field intravital imaging by two-photon-excitation digital-scanned light-sheet microscopy (2p-DSLM) with a high-pulse energy laser. Biomed. Opt. Express, 5(10), 3311–3325. https://doi.org/10.1364/BOE.5.003311


Mayer, J., Robert-Moreno, A., Danuser, R., Stein, J. V., Sharpe, J., & Swoger, J. (2014). OPTiSPIM: integrating optical projection tomography in light sheet microscopy extends specimen characterization to nonfluorescent contrasts. Opt. Lett., 39(4), 1053–1056. https://doi.org/10.1364/OL.39.001053


Mickoleit, M., Schmid, B., Weber, M., Fahrbach, F. O., Hombach, S., Reischauer, S., & Huisken, J. (2014). High-resolution reconstruction of the beating zebrafish heart. Nat. Methods, 11(9), 919–922. https://doi.org/10.1038/nmeth.3037


Mohan, K., Purnapatra, S. B., & Mondal, P. P. (2014). Three dimensional fluorescence imaging using multiple light-sheet microscopy. PLoS One, 9(6), e96551. https://doi.org/10.1371/journal.pone.0096551


Nylk, J., Mitchell, C., Vettenburg, T., Gunn-Moore, F. J., & Dholakia, K. (2014). Wavefront shaping of a Bessel light field enhances light sheet microscopy with scattered light. In SPIE BiOS (p. 89490V–89490V–8). International Society for Optics and Photonics. https://doi.org/10.1117/12.2038525


Pampaloni, F., Berge, U., Marmaras, A., Horvath, P., Kroschewski, R., & Stelzer, E. H. K. (2014). Tissue-culture light sheet fluorescence microscopy (TC-LSFM) allows long-term imaging of three-dimensional cell cultures under controlled conditions. Integr. Biol., 6(10), 988–998. https://doi.org/10.1039/C4IB00121D


Pauli, A., Norris, M. L., Valen, E., Chew, G.-L., Gagnon, J. A., Zimmerman, S., … Schier, A. F. (2014). Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science, 343(6172), 1248636. https://doi.org/10.1126/science.1248636


Pollmann, C., Hägerling, R., & Kiefer, F. (2014). Visualization of lymphatic vessel development, growth, and function. Adv. Anat. Embryol. Cell Biol., 214, 167–186. https://doi.org/10.1007/978-3-7091-1646-3_13


Pöschinger, T., Renner, A., Eisa, F., Dobosz, M., Strobel, S., Weber, T. G., … Scheuer, W. (2014). Dynamic contrast-enhanced micro-computed tomography correlates with 3-dimensional fluorescence ultramicroscopy in antiangiogenic therapy of breast cancer xenografts. Invest. Radiol., 49(7), 445–456. https://doi.org/10.1097/RLI.0000000000000038


Preibisch, S., Amat, F., Stamataki, E., Sarov, M., Singer, R. H., Myers, E., & Tomancak, P. (2014). Efficient Bayesian-based multiview deconvolution. Nat. Methods, 11(6), 645–648. https://doi.org/10.1038/nmeth.2929


Psycharakis, S., Zacharopoulos, A., Ripoll, J., Zacharakis, G., Riekher, M., & Tavernarakis, N. (2014). Optical projection tomography and light sheet microscopy for imaging in biological specimens a comparison study. In Imaging Systems and Techniques (IST), 2014 IEEE International Conference on (pp. 211–215). https://doi.org/10.1109/IST.2014.6958475


Purnapatra, S. B., Mohan, K., & Mondal, P. P. (2014). Generation of multiple sheets of light using spatial-filtering technique. Opt. Lett., 39(16), 4715–4718. https://doi.org/10.1364/OL.39.004715


Regmi, R., Mohan, K., & Mondal, P. P. (2014). High resolution light-sheet based high-throughput imaging cytometry system enables visualization of intra-cellular organelles. AIP Adv., 4(9), 97125. https://doi.org/10.1063/1.4896260


Saghafi, S., Becker, K., Hahn, C., & Dodt, H.-U. (2014). 3D-ultramicroscopy utilizing aspheric optics. J. Biophotonics, 7(1–2), 117–125. https://doi.org/10.1002/jbio.201300048


Scheul, T., Wang, I., & Vial, J.-C. (2014). STED-SPIM made simple. Opt. Express, 22(25), 30852–30864. https://doi.org/10.1364/OE.22.030852


Schmied, C., Stamataki, E., & Tomancak, P. (2014). Open-source solutions for SPIMage processing. Methods Cell Biol., 123, 505–529. https://doi.org/10.1016/B978-0-12-420138-5.00027-6


Silvestri, L., Allegra Mascaro, A. L., Costantini, I., Sacconi, L., & Pavone, F. S. (2014). Correlative two-photon and light sheet microscopy. Methods, 66(2), 268–272. https://doi.org/10.1016/j.ymeth.2013.06.013


Silvestri, L., Mascaro, A. L. A., Costantini, I., Sacconi, L., & Pavone, F. S. (2014). Exploring the brain on multiple scales with correlative two-photon and light sheet microscopy. In SPIE BiOS (p. 89480I–89480I–6). International Society for Optics and Photonics. https://doi.org/10.1117/12.2037867


Silvestri, L., Sacconi, L., & Pavone, F. S. (2014). Correcting spherical aberrations in confocal light sheet microscopy: a theoretical study. Microsc. Res. Tech., 77(7), 483–491. https://doi.org/10.1002/jemt.22330


Sinkó, J., Szabó, G., & Erdélyi, M. (2014). Ray tracing analysis of inclined illumination techniques. Opt. Express, 22(16), 18940–18948. https://doi.org/10.1364/OE.22.018940


Spille, J.-H. (2014). Three-dimensional single particle tracking in a light sheet microscope. hss.ulb.uni-bonn.de. Retrieved from http://hss.ulb.uni-bonn.de/2014/3589/3589.pdf


Stegmaier, J., Otte, J. C., Kobitski, A., Bartschat, A., Garcia, A., Nienhaus, G. U., … Mikut, R. (2014). Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks. PLoS One, 9(2), e90036. https://doi.org/10.1371/journal.pone.0090036


Strobl, F., & Stelzer, E. H. K. (2014). Non-invasive long-term fluorescence live imaging of Tribolium castaneum embryos. Development, 141(11), 2331–2338. https://doi.org/10.1242/dev.108795


Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., … Ueda, H. R. (2014). Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell, 157(3), 726–739. https://doi.org/10.1016/j.cell.2014.03.042


Swoger, J., Pampaloni, F., & Stelzer, E. H. K. (2014a). Imaging cellular spheroids with a single (selective) plane illumination microscope. Cold Spring Harb. Protoc., 2014(1), 106–113. https://doi.org/10.1101/pdb.prot080176


Swoger, J., Pampaloni, F., & Stelzer, E. H. K. (2014b). Imaging MDCK cysts with a single (selective) plane illumination microscope. Cold Spring Harb. Protoc., 2014(1), 114–118. https://doi.org/10.1101/pdb.prot080184


Swoger, J., Pampaloni, F., & Stelzer, E. H. K. (2014c). Light-sheet-based fluorescence microscopy for three-dimensional imaging of biological samples. Cold Spring Harb. Protoc., 2014(1), 1–8. https://doi.org/10.1101/pdb.top080168


Taylor, J. M. (2014). Optically gated beating-heart imaging. Front. Physiol., 5, 481. https://doi.org/10.3389/fphys.2014.00481


Udan, R. S., Piazza, V. G., Hsu, C.-W., Hadjantonakis, A.-K., & Dickinson, M. E. (2014). Quantitative imaging of cell dynamics in mouse embryos using light-sheet microscopy. Development, 141(22), 4406–4414. https://doi.org/10.1242/dev.111021


Vermeer, J. E. M., von Wangenheim, D., Barberon, M., Lee, Y., Stelzer, E. H. K., Maizel, A., & Geldner, N. (2014). A spatial accommodation by neighboring cells is required for organ initiation in Arabidopsis. Science, 343(6167), 178–183. https://doi.org/10.1126/science.1245871


Vettenburg, T., Dalgarno, H. I. C., Nylk, J., Coll-Lladó, C., Ferrier, D. E. K., Čižmár, T., … Dholakia, K. (2014). Light-sheet microscopy using an Airy beam. Nat. Methods, 11(5), 541–544. https://doi.org/10.1038/nmeth.2922


Vladimirov, N., Mu, Y., Kawashima, T., Bennett, D. V., Yang, C.-T., Looger, L. L., … Ahrens, M. B. (2014). Light-sheet functional imaging in fictively behaving zebrafish. Nat. Methods, 11(9), 883–884. https://doi.org/10.1038/nmeth.3040


Wang, D., Meza, D., Wang, Y., Gao, L., & Liu, J. T. C. (2014). Sheet-scanned dual-axis confocal microscopy using Richardson-Lucy deconvolution. Opt. Lett., 39(18), 5431–5434. https://doi.org/10.1364/OL.39.005431


Weber, M., Mickoleit, M., & Huisken, J. (2014a). Light sheet microscopy. Methods Cell Biol., 123, 193–215. https://doi.org/10.1016/B978-0-12-420138-5.00011-2


Weber, M., Mickoleit, M., & Huisken, J. (2014b). Multilayer mounting for long-term light sheet microscopy of zebrafish. J. Vis. Exp., (84), e51119. https://doi.org/10.3791/51119


Weber, T. G., Osl, F., Renner, A., Pöschinger, T., Galbán, S., Rehemtulla, A., & Scheuer, W. (2014). Apoptosis imaging for monitoring DR5 antibody accumulation and pharmacodynamics in brain tumors noninvasively. Cancer Res., 74(7), 1913–1923. https://doi.org/10.1158/0008-5472.CAN-13-3001


Wenzel, C., Riefke, B., Gründemann, S., Krebs, A., Christian, S., Prinz, F., … Steigemann, P. (2014). 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions. Exp. Cell Res., 323(1), 131–143. https://doi.org/10.1016/j.yexcr.2014.01.017


Wu, T.-F., Yen, T. M., Han, Y., Chiu, Y.-J., Lin, E. Y.-S., & Lo, Y.-H. (2014). A light-sheet microscope compatible with mobile devices for label-free intracellular imaging and biosensing. Lab Chip, 14(17), 3341–3348. https://doi.org/10.1039/C4LC00257A


Yang, Z., Prokopas, M., Nylk, J., Coll-Lladó, C., Gunn-Moore, F. J., Ferrier, D. E. K., … Dholakia, K. (2014). A compact Airy beam light sheet microscope with a tilted cylindrical lens. Biomed. Opt. Express, 5(10), 3434–3442. https://doi.org/10.1364/BOE.5.003434


Zhang, P., Goodwin, P. M., & Werner, J. H. (2014). Fast, 3D imaging via confocal line scanning of a Bessel beam using a single galvo mirror. In SPIE BiOS (p. 89471K–89471K–8). International Society for Optics and Photonics. https://doi.org/10.1117/12.2036848


Zhang, P., Goodwin, P. M., & Werner, J. H. (2014). Fast, super resolution imaging via Bessel-beam stimulated emission depletion microscopy. Opt. Express, 22(10), 12398–12409. https://doi.org/10.1364/OE.22.012398


Zhang, P., Phipps, M. E., Goodwin, P. M., & Werner, J. H. (2014). Confocal line scanning of a Bessel beam for fast 3D imaging. Opt. Lett., 39(12), 3682–3685. https://doi.org/10.1364/OL.39.003682


Zhao, M., Zhang, H., Li, Y., Ashok, A., Liang, R., Zhou, W., & Peng, L. (2014). Cellular imaging of deep organ using two-photon Bessel light-sheet nonlinear structured illumination microscopy. Biomed. Opt. Express, 5(5), 1296–1308. https://doi.org/10.1364/BOE.5.001296


Zhao, Z. W., Roy, R., Gebhardt, J. C. M., Suter, D. M., Chapman, A. R., & Xie, X. S. (2014). Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc. Natl. Acad. Sci. U. S. A., 111(2), 681–686. https://doi.org/10.1073/pnas.1318496111


Zong, W., Zhao, J., Chen, X., Lin, Y., Ren, H., Zhang, Y., … Chen, L. (2014). Two-photon three-axis digital scanned light-sheet microscopy (2P3A-DSLM). In SPIE Optical Engineering + Applications (p. 91980W–91980W–6). International Society for Optics and Photonics. https://doi.org/10.1117/12.2062690