Three-Dimensional Superresolution Microscopy Literature References

Several innovative solutions have been presented for single-molecule superresolution imaging in three dimensions, including imaging in two different focal planes, interferometry, tilted mirrors, and convolution of the point-spread function Fourier transform with a more complex mathematical model (such as the double-helix point-spread function) using a spatial light modulator. In addition, structured illumination and advanced point-spread function modifying techniques, such as stimulated emission depletion (STED), ground state depletion (GSD) and 4Pi microscopy have also been utilized to probe the three-dimensional structure of biological specimens.

Recommended Literature

Dedecker, P., Flors, C., Hotta, J. I., Uji-i, H. and Hofkens, J. 3D nanoscopy: Bringing biological nanostructures into sharp focus. Angewandte Chemie International Edition 46: 8330-8332 (2007).
Dertinger, T., Colyer, R., Iyer, G., Weiss, S. and Enderlein, J. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). Proceedings of the National Academy of Sciences (USA) 106: 22287-22292 (2009).
Huang, B., Jones, S. A., Brandenburg, B. and Zhuang, X. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nature Methods5: 1047-1052 (2008).
Huang, B., Wang, W., Bates, M. and Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319: 810-813 (2008).
Hell, S. W., Schmidt, R. and Egner, A. Diffraction-unlimited three-dimensional optical nanoscopy with opposing lenses. Nature Photonics 3: 381-387 (2009).
Juette, M. F., Gould, T. J., Lessard, M. D., Mlodzianoski, M. J., Nagpure, B. S., Bennett, B. T., Hess, S. T. and Bewersdorf, J. Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nature Methods 5: 527-529 (2008).
Lew, M. D., Thompson, M. A., Badieirostami, M. and Moerner, W. E. In vivo three-dimensional superresolution fluorescence tracking using a double-helix point spread function.Proceedings of SPIE 7571: 75710Z-13 (2010).
Pavani, S. R. P., Greengard, A. and Piestun, R. Three-dimensional localization with nanometer accuracy using a detector-limited double-helix point spread function system.Applied Physics Letters 95: 021103-3 (2009).
Pavani, S. R. P., Thompson, M. A., Biteen, J. S., Lord, S. J., Liu, N., Twieg, R. J., Piestun, R. and Moerner, W. E. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proceedings of the National Academy of Sciences (USA) 106: 2995-2999 (2009).
Punge, A., Rizzoli, S. O., Jahn, R., Wildanger, J. D., Meyer, L., Schonle, A., Kastrup, L. and Hell, S. W. 3D reconstruction of high-resolution STED microscope images. Microscopy Research and Technique 71: 644-650 (2008).
Ram S., Prabhat, P., Chao, J., Ward, E. S. and Ober, R. J. High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells. Biophysical Journal 95: 6025-6043 (2008).
Schermelleh, L., Carlton, P. M., Haase, S., Shao, L., Winoto, L., Kner, P., Burke, B., Cardoso, M. C., Agard, D.A., Gustafsson, M. G. L., Leonhardt, H. and Sedat, J. W. Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320:1332-1336 (2008).
Schrader, M., Hell, S. W. and van der Voort, H. T. M. Three-dimensional super-resolution with a 4pi-confocal microscope using image restoration. Journal of Applied Physics 84: 4033-4042 (1998).
Shtengel, G., Galbraith, J. A., Galbraith, C. G., Lippincott-Schwartz, J., Gillette, J. M., Manley, S., Sougrat, R., Waterman, C. M., Kanchanawong, P., Davidson, M. W., Fetter, R. D. and Hess, H. F. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proceedings of the National Academy of Sciences (USA) 106: 3125-3130 (2009).
Vaziri, A., Tang, J., Shroff, H. and Shank, C. V. Multilayer three-dimensional super resolution imaging of thick biological samples. Proceedings of the National Academy of Sciences (USA) 105: 20221-20226 (2008).
van Oijen, A. M., Kohler, J., Schmidt, J., Muller, M. and Brakenhoff, G. J. 3-dimensional super-resolution by spectrally selective imaging. Chemical Physics Letters 292: 183-187 (1998).
von Middendorff, C., Egner, A., Geisler, C., Hell, S. W. and Schonle, A. Isotropic 3D nanoscopy based on single emitter switching. Optics Express 16: 20774-20788 (2008).
Wildanger, D., Medda, R., Kastrup, L. and Hell, S. W. A compact STED microscope providing 3D nanoscale resolution. Journal of Microscopy 236: 35-43 (2009).

Additional Literature Sources

Bornfleth, H., Satzler, K., Eils, R. and Cremer, C. High-precision distance measurements and volume-conserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy. Journal of Microscopy 189: 118-136 (1998).
Chao, J., Ram, S., Ward, E. S. and Ober, R. J. A comparative study of high resolution microscopy imaging modalities using a three-dimensional resolution measure. Optics Express 17: 24377-24402 (2009).
Downing, K. H., Sui, H. and Auer, M. Electron tomography: A 3D view of the subcellular world. Analytical Chemistry 79: 7949-7957 (2007).
Fitzgibbon, J., Bell, K., King, E. and Oparka, K. Super-resolution imaging of plasmodesmata using three-dimensional structured illumination microscopy. Plant Physiology 153: 1453-1463 (2010).
Frohn, J. T., Knapp, H. F. and Stemmer, A. Three-dimensional resolution enhancement in fluorescence microscopy by harmonic excitation. Optics Letters 26: 828-830 (2001).
Gustafsson, M. G. L., Agard, D. A. and Sedat, J. W. Sevenfold improvement of axial resolution in 3D wide-field microscopy using two objective lenses. Proceedings of SPIE2412: 147-155 (1995).
Gustafsson, M. G. L., Agard, D. A. and Sedat, J. W. Doubling the lateral resolution of wide-field fluorescence microscopy using structured illumination. Proceedings of SPIE 3919:141-150 (2008).
Haeberle, O., Xu, C., Dieterlen, A. and Jacquey, S. Multiple-objective microscopy with three-dimensional resolution near 100 nm and a long working distance. Optics Letters 26: 1684-1686 (2001).
Harke, B., Ullal, C. K., Keller, J. and Hell, S. W. Three-dimensional nanoscopy of colloidal crystals. Nano Letters 8: 1309-1313 (2008).
Hellriegel, C. and Gratton, E. Real-time multi-parameter spectroscopy and localization in three-dimensional single-particle tracking. Journal of the Royal Society Interface 6: S3-S14 (2009).
Helmstaedter, M., Briggman, K. L. and Denk, W. 3D structural imaging of the brain with photons and electrons. Current Opinion in Neurobiology 18: 633-641 (2008).
Holtzer, L., Meckel, T. and Schmidt, T. Nanometric three-dimensional tracking of individual quantum dots in cells. Applied Physics Letters 90: 053902-3 (2007).
Kao, H. P. and Verkman, A. S. Tracking of single fluorescent particles in three dimensions: Use of cylindrical optics to encode particle position. Biophysical Journal 67: 1291-1300 (1994).
Lang, M., Jegou, T., Chung, I., Richter, K., Munch, S., Udvarhelyi, A., Cremer, C., Hemmerich, P., Engelhardt, J., Hell, S. W. and Rippe, K. Three-dimensional organization of promyelocytic leukemia nuclear bodies. Journal of Cell Science 123: 392-400 (2010).
Mlodzianoski, M. J., Juette, M. F., Beane, G. L. and Bewersdorf, J. Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy. Optics Express 17: 8264-8277 (2009).
Nagerl, U. V., Willig, K. I., Hein, B., Hell, S. W. and Bonhoeffer, T. Live-cell imaging of dendritic spines by STED microscopy. Proceedings of the National Academy of Sciences (USA)105: 18982-18987 (2008).
Oron, D., Tal, E. and Silberberg, Y. Scanningless depth-resolved microscopy. Optics Express 13: 1468-1476 (2005).
Pavani, S. R. P., DeLuca, J. G. and Piestun, R. Polarization sensitive, three-dimensional, single-molecule imaging of cells with a double-helix system. Optics Express 17: 19644-19655 (2009).
Ploeger, L., Dullens, H., Huisman, A. and van Diest, P. Fluorescent stains for quantifications of DNA by confocal laser scanning microscopy in 3-D. Biotechnic and Histochemistry 83:63-69 (2008).
Prabhat, P., Ram, S., Ward, E. S. and Ober, R. J. Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions.IEEE Transactions on Nanobioscience 3: 237-242 (2004).
Prabhat, P., Ram, S., Ward, E. S. and Ober, R. J. Simultaneous imaging of several focal planes in fluorescence microscopy for the study of cellular dynamics in 3D. Proceedings of SPIE 6090: 60900L-7 (2006).
Ram S., Chao, J., Prabhat, P., Ward, E. S. and Ober, R. J. A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking. Proceedings of SPIE 6443: 64430D-7 (2007).
Rodriguez, P. F. G., Sepulveda, E., Dubertret, B. and Loriette, V. Axial coding in full-field microscopy using three-dimensional structured illumination implemented with no moving parts. Optics Letters 33: 1617-1619 (2008).
Schmidt, R., Wurm, C. A., Jakobs, S., Engelhardt, J., Egner, A. and Hell, S. W. Spherical nanosized focal spot unravels the interior of cells. Nature Methods 5: 539-544 (2008).
Shaevitz, J. W. Super-resolution for a 3D world. Nature Methods 5: 471-472 (2008).
Shao, L., Isaac, B., Uzawa, S., Agard, D. A., Sedat, J. W. and Gustafsson, M. C. L. I5S: Wide-field light microscopy with 100-nm-scale resolution in three dimensions. Biophysical Journal 94: 4971-4983 (2008).
Speidel, M., Jonas, A. and Florin, E. L. Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging. Optics Letters28: 69-71 (2003).
Tang, J., Akerboom, J., Vaziri, A., Looger, L. L. and Shank, C. V. Near-isotropic 3D optical nanoscopy with photon-limited chromophores. Proceedings of the National Academy of Sciences (USA) 107: 10068-10073 (2010).
Thompson, R. E., Lew, M. D., Badieirostami, M. and Moerner, W. E. Localizing and tracking single nanoscale emitters in three dimensions with high spatiotemporal resolution using a double-helix point spread function. Nano Letters 10: 211-218 (2010).
Toprak, E., Balci, H., Blehm, B. H. and Selvin, P. R. Three-dimensional particle tracking via bifocal imaging. Nano Letters 7: 2043-2045 (2007).
Weninger, W. J., Geyer, S. H., Mohun, T. J., Rasskin-Gutman, D., Matsui, T., Ribeiro, I., Costa, L. D., Izpisua-Belmonte, J. C. and Muller, G. B. High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology. Anatomy and Embryology 211: 213-221 (2006).
Wilson, T., Neil, M. A. A. and Juskaitis, R. Real-time three-dimensional imaging of macroscopic structures. Journal of Microscopy 191: 116-118 (1998).

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