Paper Roundup – November 2014

  • An optimized immunostaining and clearing method, iDISCO, for immunofluorescence imaging of large whole-mount samples [1]
  • Thiol-driven switching of mCherry for super-resolution imaging [2]
  • A review of various software tools for image analysis. It seems difficult to do justice to the full complexity of the available tools in a short article, but this may be a good starting point if you’re looking for an image analysis tool [3]
  • A spectral imaging approach to FRET analysis [3]
  • Tomographic imaging of infrared absorption in a plant cell [4]
  • Fluctuation spectroscopy applied to light sheet data for measuring molecular transport in cells [5]
  • A nice news and views summarizing the many clearing techniques currently available [6]
  • A set of protocols for advanced usage of the Micro-manager software [7]
  • Uniquely labeling cells by stochastic uptake of quantum dots [8]
  • A very wide field of view two-photon microscope [9]
  • Cell-penetrating peptides, fused to LifeAct and photoswitchable dyes, for live cell super-resolution imaging [10]
  • A red fluorescent protein pH indicator [11]


  1. N. Renier, Z. Wu, D. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, "iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging", Cell, vol. 159, pp. 896-910, 2014.
  2. C.M. Winterflood, and H. Ewers, "Single-Molecule Localization Microscopy using mCherry", ChemPhysChem, vol. 15, pp. 3447-3451, 2014.
  3. V. WIESMANN, D. FRANZ, C. HELD, C. MÜNZENMAYER, R. PALMISANO, and T. WITTENBERG, "Review of free software tools for image analysis of fluorescence cell micrographs", Journal of Microscopy, vol. 257, pp. 39-53, 2014.
  4. L. Quaroni, M. Obst, M. Nowak, and F. Zobi, "Three-Dimensional Mid-Infrared Tomographic Imaging of Endogenous and Exogenous Molecules in a Single Intact Cell with Subcellular Resolution", Angewandte Chemie International Edition, vol. 54, pp. 318-322, 2014.
  5. P.N. Hedde, M. Stakic, and E. Gratton, "Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination", Scientific Reports, vol. 4, 2014.
  6. B. Höckendorf, L.D. Lavis, and P.J. Keller, "Making biology transparent", Nature Biotechnology, vol. 32, pp. 1104-1105, 2014.
  7. A.D. Edelstein, M.A. Tsuchida, N. Amodaj, H. Pinkard, R.D. Vale, and N. Stuurman, "Advanced methods of microscope control using μManager software", Journal of Biological Methods, vol. 1, pp. 10, 2014.
  8. P. Rees, J.W. Wills, M.R. Brown, J. Tonkin, M.D. Holton, N. Hondow, A.P. Brown, R. Brydson, V. Millar, A.E. Carpenter, and H.D. Summers, "Nanoparticle vesicle encoding for imaging and tracking cell populations", Nature Methods, vol. 11, pp. 1177-1181, 2014.
  9. J.N. Stirman, I.T. Smith, M.W. Kudenov, and S.L. Smith, "Wide field-of-view, twin-region two-photon imaging across extended cortical networks", 2014.
  10. D. Pan, Z. Hu, F. Qiu, Z. Huang, Y. Ma, Y. Wang, L. Qin, Z. Zhang, S. Zeng, and Y. Zhang, "A general strategy for developing cell-permeable photo-modulatable organic fluorescent probes for live-cell super-resolution imaging", Nature Communications, vol. 5, 2014.
  11. Y. Shen, M. Rosendale, R.E. Campbell, and D. Perrais, "pHuji, a pH-sensitive red fluorescent protein for imaging of exo- and endocytosis", Journal of Cell Biology, vol. 207, pp. 419-432, 2014.