Paper Roundup – March 2015

  • A spinning-disk confocal based super-resolution system, giving a fast 2-fold improvement in resolution [1]
  • PALMsiever: a localization microscopy tool implementing a number of algorithms for drift correction, clustering, and rendering of localization microscopy data [2]
  • An image-based microfluidic screen for cell deformation [3]
  • Six-color imaging using narrow-band filter sets [4]
  • 3D particle tracking using phase-contrast holography [5]
  • A new super-resolution approach, analogous to STED, that uses a transiently activated quencher dye, whose absorption and quenching is light-dependent [6]
  • A protease reporter based on conversion of iFP from a non-fluorescent to a fluorescent state on protease cleavage [7]
  • Osmium tetroxide fixable mEos4 proteins for correlative super-resolution microscopy and EM [8]
  • A simple chemical modification of many common dyes dramatically improves their quantum yield [9]
  • Ratiometric biosensors by dimeric partner exchange [10]
  • A simplified CLARITY protocol for brain imaging [11]
  • Following translation of RNA by removal of a bound fluorescent protein by the translating ribosome [12]
  • Single molecule imaging of DNA-bound proteins by using energy transfer from a DNA intercalating dye to activate a fluorescent label on a protein bound to the DNA [13]
  • Multicolor CRISPR labeling of chromosomal loci [14]
  • Make your own gridded coverslips using electron beam deposition of metal [15]


  1. S. Hayashi, and Y. Okada, "Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics", Molecular Biology of the Cell, vol. 26, pp. 1743-1751, 2015.
  2. T. Pengo, S.J. Holden, and S. Manley, "PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy", Bioinformatics, vol. 31, pp. 797-798, 2014.
  3. O. Otto, P. Rosendahl, A. Mietke, S. Golfier, C. Herold, D. Klaue, S. Girardo, S. Pagliara, A. Ekpenyong, A. Jacobi, M. Wobus, N. Töpfner, U.F. Keyser, J. Mansfeld, E. Fischer-Friedrich, and J. Guck, "Real-time deformability cytometry: on-the-fly cell mechanical phenotyping", Nature Methods, vol. 12, pp. 199-202, 2015.
  4. S. Kijani, U. Yrlid, M. Heyden, M. Levin, J. Borén, and P. Fogelstrand, "Filter-Dense Multicolor Microscopy", PLOS ONE, vol. 10, pp. e0119499, 2015.
  5. F. Cheong, C. Wong, Y. Gao, M. Nai, Y. Cui, S. Park, L. Kenney, and C. Lim, "Rapid, High-Throughput Tracking of Bacterial Motility in 3D via Phase-Contrast Holographic Video Microscopy", Biophysical Journal, vol. 108, pp. 1248-1256, 2015.
  6. T. Rosales, D.L. Sackett, J. Xu, Z. Shi, B. Xu, H. Li, G. Kaur, E. Frohart, N. Shenoy, S.M. Cheal, H. Wu, A.E. Dulcey, Y. Hu, C. Li, K. Lane, G.L. Griffiths, and J.R. Knutson, "STAQ: A route toward low power, Multicolor nanoscopy", Microscopy Research and Technique, vol. 78, pp. 343-355, 2015.
  7. T. To, B.J. Piggott, K. Makhijani, D. Yu, Y.N. Jan, and X. Shu, "Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo", Proceedings of the National Academy of Sciences, vol. 112, pp. 3338-3343, 2015.
  8. M.G. Paez-Segala, M.G. Sun, G. Shtengel, S. Viswanathan, M.A. Baird, J.J. Macklin, R. Patel, J.R. Allen, E.S. Howe, G. Piszczek, H.F. Hess, M.W. Davidson, Y. Wang, and L.L. Looger, "Fixation-resistant photoactivatable fluorescent proteins for CLEM", Nature Methods, vol. 12, pp. 215-218, 2015.
  9. J.B. Grimm, B.P. English, J. Chen, J.P. Slaughter, Z. Zhang, A. Revyakin, R. Patel, J.J. Macklin, D. Normanno, R.H. Singer, T. Lionnet, and L.D. Lavis, "A general method to improve fluorophores for live-cell and single-molecule microscopy", Nature Methods, vol. 12, pp. 244-250, 2015.
  10. Y. Ding, J. Li, J.R. Enterina, Y. Shen, I. Zhang, P.H. Tewson, G.C.H. Mo, J. Zhang, A.M. Quinn, T.E. Hughes, D. Maysinger, S.C. Alford, Y. Zhang, and R.E. Campbell, "Ratiometric biosensors based on dimerization-dependent fluorescent protein exchange", Nature Methods, vol. 12, pp. 195-198, 2015.
  11. H. Zheng, and L. Rinaman, "Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain", Brain Structure and Function, vol. 221, pp. 2375-2383, 2015.
  12. J.M. Halstead, T. Lionnet, J.H. Wilbertz, F. Wippich, A. Ephrussi, R.H. Singer, and J.A. Chao, "An RNA biosensor for imaging the first round of translation from single cells to living animals", Science, vol. 347, pp. 1367-1671, 2015.
  13. H. Geertsema, A. Schulte, L. Spenkelink, W. McGrath, S. Morrone, J. Sohn, W. Mangel, A. Robinson, and A. van Oijen, "Single-Molecule Imaging at High Fluorophore Concentrations by Local Activation of Dye", Biophysical Journal, vol. 108, pp. 949-956, 2015.
  14. H. Ma, A. Naseri, P. Reyes-Gutierrez, S.A. Wolfe, S. Zhang, and T. Pederson, "Multicolor CRISPR labeling of chromosomal loci in human cells", Proceedings of the National Academy of Sciences, vol. 112, pp. 3002-3007, 2015.
  15. L. Benedetti, E. Sogne, S. Rodighiero, D. Marchesi, P. Milani, and M. Francolini, "Customized patterned substrates for highly versatile correlative light-scanning electron microscopy", Scientific Reports, vol. 4, 2014.