Paper Roundup: October 2015

  • Using the wavelength dependence of the evanescent field depth to measure the height of molecules above the coverslip [1]
  • Automated super-resolution imaging of synapses in large neuronal volumes [2]
  • A software pipeline for efficient processing of large-scale light-sheet data [3]
  • Fast Fourier Ptychography [4]
  • A 2-photon microscope with large travel and rotational range [5]
  • A compact micrsocope using an electrically tunable lens for focusing [6]
  • Protocols for clearing with CUBIC [7]
  • Multi-color STORM with spectral detection [8]
  • Adaptive optics for two-photon microscopy using a liquid crystal on silicon modulator and a hill climbing algorithm [9]
  • A microscope optimized for low light, low magnification imaging, using a short focal length tube lens [10]
  • A fluidic light sheet system for sample delivery through fluidics [11]
  • Protocols for passive CLARITY clearing [12]
  • A protocol for intravital imaging of the beating mouse heart [13]
  • Super-resolution imaging of click-chemistry tagged proteins compared with that of fluorescent proteins [14]
  • The 2015 super-resolution roadmap [15]


  1. D.R. Stabley, T. Oh, S.M. Simon, A.L. Mattheyses, and K. Salaita, "Real-time fluorescence imaging with 20 nm axial resolution", Nature Communications, vol. 6, 2015.
  2. Y. Sigal, C. Speer, H. Babcock, and X. Zhuang, "Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging", Cell, vol. 163, pp. 493-505, 2015.
  3. F. Amat, B. Höckendorf, Y. Wan, W.C. Lemon, K. McDole, and P.J. Keller, "Efficient processing and analysis of large-scale light-sheet microscopy data", Nature Protocols, vol. 10, pp. 1679-1696, 2015.
  4. L. Tian, Z. Liu, L. Yeh, M. Chen, J. Zhong, and L. Waller, "Computational illumination for high-speed in vitro Fourier ptychographic microscopy", Optica, vol. 2, pp. 904, 2015.
  5. J.M. Mayrhofer, F. Haiss, D. Haenni, S. Weber, M. Zuend, M.J.P. Barrett, K.D. Ferrari, P. Maechler, A.S. Saab, J.L. Stobart, M.T. Wyss, H. Johannssen, H. Osswald, L.M. Palmer, V. Revol, C. Schuh, C. Urban, A. Hall, M.E. Larkum, E. Rutz-Innerhofer, H.U. Zeilhofer, U. Ziegler, and B. Weber, "Design and performance of an ultra-flexible two-photon microscope for in vivo research", Biomedical Optics Express, vol. 6, pp. 4228, 2015.
  6. Z. Wang, M. Lei, B. Yao, Y. Cai, Y. Liang, Y. Yang, X. Yang, H. Li, and D. Xiong, "Compact multi-band fluorescent microscope with an electrically tunable lens for autofocusing", Biomedical Optics Express, vol. 6, pp. 4353, 2015.
  7. E.A. Susaki, K. Tainaka, D. Perrin, H. Yukinaga, A. Kuno, and H.R. Ueda, "Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging", Nature Protocols, vol. 10, pp. 1709-1727, 2015.
  8. Z. Zhang, S.J. Kenny, M. Hauser, W. Li, and K. Xu, "Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy", Nature Methods, vol. 12, pp. 935-938, 2015.
  9. M. SKORSETZ, P. ARTAL, and J.M. BUENO, "Performance evaluation of a sensorless adaptive optics multiphoton microscope", Journal of Microscopy, vol. 261, pp. 249-258, 2015.
  10. T.J. Kim, S. Tuerkcan, A. Ceballos, and G. Pratx, "Modular platform for low-light microscopy", Biomedical Optics Express, vol. 6, pp. 4585, 2015.
  11. E.J. Gualda, H. Pereira, T. Vale, M.F. Estrada, C. Brito, and N. Moreno, "SPIM-fluid: open source light-sheet based platform for high-throughput imaging", Biomedical Optics Express, vol. 6, pp. 4447, 2015.
  12. J.B. Treweek, K.Y. Chan, N.C. Flytzanis, B. Yang, B.E. Deverman, A. Greenbaum, A. Lignell, C. Xiao, L. Cai, M.S. Ladinsky, P.J. Bjorkman, C.C. Fowlkes, and V. Gradinaru, "Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping", Nature Protocols, vol. 10, pp. 1860-1896, 2015.
  13. C. Vinegoni, A.D. Aguirre, S. Lee, and R. Weissleder, "Imaging the beating heart in the mouse using intravital microscopy techniques", Nature Protocols, vol. 10, pp. 1802-1819, 2015.
  14. I.C. Vreja, I. Nikić, F. Göttfert, M. Bates, K. Kröhnert, T.F. Outeiro, S.W. Hell, E.A. Lemke, and S.O. Rizzoli, "Super-resolution Microscopy of Clickable Amino Acids Reveals the Effects of Fluorescent Protein Tagging on Protein Assemblies", ACS Nano, vol. 9, pp. 11034-11041, 2015.
  15. S.W. Hell, S.J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M.J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S.J. Davis, C. Eggeling, D. Klenerman, K.I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, "The 2015 super-resolution microscopy roadmap", Journal of Physics D: Applied Physics, vol. 48, pp. 443001, 2015.

A 4 Gigapixel image of a human brain section

I’ve been working with a group at UCSF that studies neurodegenerative diseases in humans. They have access to a large number of postmortem human brains that they would like very much to image to look at markers of neurodegenerative diseases. As you might imagine, this is not easy. The sections are on the order of 10 cm by 7 cm – not the sort of thing you usually image on a microscope.

Recently, we got a DS-Ri2 camera from Nikon. This is a 16 megapixel color camera with 7.7 μm pixels. Combined with a 2.5x coupling lens, we get a pixel size of 1.5 μm, which gives us diffraction limited imaging with our 2x / 0.1 NA objective. Capturing 16 megapixels at a time makes it much faster to capture a sample this large, and we were able to capture the entire image in about 15 minutes. It would have been faster except that the section was wavy and so we needed to use image-based autofocusing to correct the focus every few images. The resulting image is just under 4 gigapixels; acquisition and stitching were done in NIS-Elements, which had no problem with this large of an image. The edges of the brain are cut off because we ran into the limits of the stage travel.

I’ve uploaded the image to Gigapan and you can view it below:

Paper Roundup: September 2015

  • A low-noise semiconductor photodetector that may outperform APDs [1]
  • A hyperspectral light sheet microscope [2]
  • Two-photon-like imaging using a photoswitchable fluorescent protein [3]
  • Confocal scanning by tilting of a refractive element [4]
  • ScaleS, an improved version of Scale for clearing brains and tissues; it does not cause tissue expansion or shrinkage and preserves fluorescent proteins well [5]
  • Optimal dyes for dSTORM by reductive caging [6]
  • Photoactivatible calcium reporters [7]
  • Ultrafast STED microscopy [8]
  • Monomeric, cysteine free fluorescent proteins for expression in oxidizing environments [9]
  • Label-free imaging of DNA with stimulated Raman scattering microscopy [10]
  • A review of cellphones for microscopy [11]


  1. Y. Liu, L. Yan, A.C. Zhang, D. Hall, I.A. Niaz, Y. Zhou, L.J. Sham, and Y. Lo, "Cycling excitation process: An ultra efficient and quiet signal amplification mechanism in semiconductor", Applied Physics Letters, vol. 107, pp. 053505, 2015.
  2. W. Jahr, B. Schmid, C. Schmied, F.O. Fahrbach, and J. Huisken, "Hyperspectral light sheet microscopy", Nature Communications, vol. 6, 2015.
  3. M. Ingaramo, A.G. York, E.J. Andrade, K. Rainey, and G.H. Patterson, "Two-photon-like microscopy with orders-of-magnitude lower illumination intensity via two-step fluorescence", Nature Communications, vol. 6, 2015.
  4. A. Tsikouras, R. Berman, D.W. Andrews, and Q. Fang, "High-speed multifocal array scanning using refractive window tilting", Biomedical Optics Express, vol. 6, pp. 3737, 2015.
  5. H. Hama, H. Hioki, K. Namiki, T. Hoshida, H. Kurokawa, F. Ishidate, T. Kaneko, T. Akagi, T. Saito, T. Saido, and A. Miyawaki, "ScaleS: an optical clearing palette for biological imaging", Nature Neuroscience, vol. 18, pp. 1518-1529, 2015.
  6. M. Lehmann, B. Gottschalk, D. Puchkov, P. Schmieder, S. Schwagerus, C.P.R. Hackenberger, V. Haucke, and J. Schmoranzer, "Multicolor Caged dSTORM Resolves the Ultrastructure of Synaptic Vesicles in the Brain", Angewandte Chemie International Edition, vol. 54, pp. 13230-13235, 2015.
  7. S. Berlin, E.C. Carroll, Z.L. Newman, H.O. Okada, C.M. Quinn, B. Kallman, N.C. Rockwell, S.S. Martin, J.C. Lagarias, and E.Y. Isacoff, "Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging", Nature Methods, vol. 12, pp. 852-858, 2015.
  8. J. Schneider, J. Zahn, M. Maglione, S.J. Sigrist, J. Marquard, J. Chojnacki, H. Kräusslich, S.J. Sahl, J. Engelhardt, and S.W. Hell, "Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics", Nature Methods, vol. 12, pp. 827-830, 2015.
  9. L.M. Costantini, M. Baloban, M.L. Markwardt, M. Rizzo, F. Guo, V.V. Verkhusha, and E.L. Snapp, "A palette of fluorescent proteins optimized for diverse cellular environments", Nature Communications, vol. 6, 2015.
  10. F. Lu, S. Basu, V. Igras, M.P. Hoang, M. Ji, D. Fu, G.R. Holtom, V.A. Neel, C.W. Freudiger, D.E. Fisher, and X.S. Xie, "Label-free DNA imaging in vivo with stimulated Raman scattering microscopy", Proceedings of the National Academy of Sciences, vol. 112, pp. 11624-11629, 2015.
  11. R. DENDERE, N. MYBURG, and T. DOUGLAS, "A review of cellphone microscopy for disease detection", Journal of Microscopy, vol. 260, pp. 248-259, 2015.