Paper Roundup: September 2013

  • A short review of tissue clearing methods. [1]
  • Optimizing FRET probes by driving interaction of the donor and acceptor in a favorable FRET geometry, either by electrostatic interaction or by using weak heterodimerization domains. [2]
  • A review on alternating laser excitation (ALEX) for FRET microscopy. [3]
  • Silicon nanoparticles: a novel bright, nonblinking probe for single molecule studies (essentially a non-blinking Qdot replacement). [4]
  • Fluorescent nanodiamonds have been used for long-term tracking of lung stem cells in mice. [5]
  • A new red-shifted channelrhodopsin. [6]
  • Journal of Optics has a special issue on high-resolution (super-resolution) optical imaging.
  • A comparison of single particle tracking and temporal image correlation spectroscopy for monitoring diffusion and transport. [7]
  • A comprehensive review of fluorescent proteins for super-resolution imaging. [8]
  • SuperNova: a monomeric version of KillerRed for chromophore-assisted laser inactivation. [9]
  • A frequency domain approach for very high speed imaging, where different pixels are excited at different frequencies. The fluorescence emission is recorded on a PMT and signals at different frequencies are extracted to recover the image. It runs at over 4000 fps for 200 x 92 pixels. [10]
  • A wide-field two-photon approach for neuronal imaging in C. elegans. [11]


  1. D.A. Yushchenko, and C. Schultz, "Tissue Clearing for Optical Anatomy", Angewandte Chemie International Edition, vol. 52, pp. 10949-10951, 2013.
  2. R. Grünberg, J.V. Burnier, T. Ferrar, V. Beltran-Sastre, F. Stricher, A.M. van der Sloot, R. Garcia-Olivas, A. Mallabiabarrena, X. Sanjuan, T. Zimmermann, and L. Serrano, "Engineering of weak helper interactions for high-efficiency FRET probes", Nature Methods, vol. 10, pp. 1021-1027, 2013.
  3. J. Hohlbein, T.D. Craggs, and T. Cordes, "Alternating-laser excitation: single-molecule FRET and beyond", Chem. Soc. Rev., vol. 43, pp. 1156-1171, 2014.
  4. H. Nishimura, K. Ritchie, R.S. Kasai, M. Goto, N. Morone, H. Sugimura, K. Tanaka, I. Sase, A. Yoshimura, Y. Nakano, T.K. Fujiwara, and A. Kusumi, "Biocompatible fluorescent silicon nanocrystals for single-molecule tracking and fluorescence imaging", The Journal of Cell Biology, vol. 202, pp. 967-983, 2013.
  5. T. Wu, Y. Tzeng, W. Chang, C. Cheng, Y. Kuo, C. Chien, H. Chang, and J. Yu, "Tracking the engraftment and regenerative capabilities of transplanted lung stem cells using fluorescent nanodiamonds", Nature Nanotechnology, vol. 8, pp. 682-689, 2013.
  6. J.Y. Lin, P.M. Knutsen, A. Muller, D. Kleinfeld, and R.Y. Tsien, "ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation", Nature Neuroscience, vol. 16, pp. 1499-1508, 2013.
  7. F. LUND, and D. WÜSTNER, "A comparison of single particle tracking and temporal image correlation spectroscopy for quantitative analysis of endosome motility", Journal of Microscopy, vol. 252, pp. 169-188, 2013.
  8. K. Nienhaus, and G. Ulrich Nienhaus, "Fluorescent proteins for live-cell imaging with super-resolution", Chem. Soc. Rev., vol. 43, pp. 1088-1106, 2014.
  9. K. Takemoto, T. Matsuda, N. Sakai, D. Fu, M. Noda, S. Uchiyama, I. Kotera, Y. Arai, M. Horiuchi, K. Fukui, T. Ayabe, F. Inagaki, H. Suzuki, and T. Nagai, "SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation", Scientific Reports, vol. 3, 2013.
  10. E.D. Diebold, B.W. Buckley, D.R. Gossett, and B. Jalali, "Digitally synthesized beat frequency multiplexing for sub-millisecond fluorescence microscopy", Nature Photonics, vol. 7, pp. 806-810, 2013.
  11. T. Schrödel, R. Prevedel, K. Aumayr, M. Zimmer, and A. Vaziri, "Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light", Nature Methods, vol. 10, pp. 1013-1020, 2013.

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