Paper Roundup – August 2016

  • A new far-red fluorescent protein that uses biliverdin as a chromophore and is brighter than existing far red FPs [1]
  • A review of quantum dot blinking and how to control it [2]
  • Photoactivatible versions of the Janelia Farms (JF) dyes for single molecule imaging [3]
  • Comparison of different clearing methods for mouse embryos and hearts [4]
  • A malachite green fluorogen-activating protein that outperforms Cy5 for single molecule imaging [5]
  • A general model for counting molecules in single-molecule microscopy [6]
  • Stimulated Raman scattering imaging of bioorthogonal probes [7]
  • Multiview image capture and fusion for resolution improvement in widefield and light sheet microscopy [8]
  • Combining photoswitching and analytical ultracentrifugation to interrogate complex binding equilibria [9]
  • A simplified CLARITY clearing method, eliminating the need for removal of oxygen prior to polymerization [10]
  • A custom two-photon microscope for wide field-of-view imaging [11]
  • Pulsed illumination reduces phototoxicity and photobleaching [12]
  • Identifying clusters in localization microscopy images by varying labeling density [13]
  • Reversible cryo-arrest of cells by chilling to -45°C on a microscope [14]
  • Correlation between hybridizations to measure transcript number by imaging [15]
  • Using a speckle scrambler to improve illumination uniformity in TIRF and localization microscopy [16]
  • Monomeric near-infrared fluorescent proteins [17]


  1. E.A. Rodriguez, G.N. Tran, L.A. Gross, J.L. Crisp, X. Shu, J.Y. Lin, and R.Y. Tsien, "A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein", Nature Methods, vol. 13, pp. 763-769, 2016.
  2. A.L. Efros, and D.J. Nesbitt, "Origin and control of blinking in quantum dots", Nature Nanotechnology, vol. 11, pp. 661-671, 2016.
  3. J.B. Grimm, B.P. English, A.K. Muthusamy, B.P. Mehl, P. Dong, T.A. Brown, Z. Liu, T. Lionnet, and L.D. Lavis, "Bright photoactivatable fluorophores for single-molecule imaging", 2016.
  4. H. Kolesová, M. Čapek, B. Radochová, J. Janáček, and D. Sedmera, "Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts", Histochemistry and Cell Biology, vol. 146, pp. 141-152, 2016.
  5. S. Saurabh, A.M. Perez, C.J. Comerci, L. Shapiro, and W.E. Moerner, "Super-resolution Imaging of Live Bacteria Cells Using a Genetically Directed, Highly Photostable Fluoromodule", Journal of the American Chemical Society, vol. 138, pp. 10398-10401, 2016.
  6. G. Hummer, F. Fricke, and M. Heilemann, "Model-independent counting of molecules in single-molecule localization microscopy", Molecular Biology of the Cell, vol. 27, pp. 3637-3644, 2016.
  7. L. Wei, F. Hu, Z. Chen, Y. Shen, L. Zhang, and W. Min, "Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes", Accounts of Chemical Research, vol. 49, pp. 1494-1502, 2016.
  8. Y. Wu, P. Chandris, P.W. Winter, E.Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J.M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C.M. Waterman, K.S. Ramamurthi, P.J. La Riviere, and H. Shroff, "Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy", Optica, vol. 3, pp. 897, 2016.
  9. H. Zhao, Y. Fu, C. Glasser, E.J. Andrade Alba, M.L. Mayer, G. Patterson, and P. Schuck, "Monochromatic multicomponent fluorescence sedimentation velocity for the study of high-affinity protein interactions", eLife, vol. 5, 2016.
  10. K. Sung, Y. Ding, J. Ma, H. Chen, V. Huang, M. Cheng, C.F. Yang, J.T. Kim, D. Eguchi, D. Di Carlo, T.K. Hsiai, A. Nakano, and R.P. Kulkarni, "Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping", Scientific Reports, vol. 6, 2016.
  11. J.N. Stirman, I.T. Smith, M.W. Kudenov, and S.L. Smith, "Wide field-of-view, multi-region, two-photon imaging of neuronal activity in the mammalian brain", Nature Biotechnology, vol. 34, pp. 857-862, 2016.
  12. C. Boudreau, T.(. Wee, Y.(. Duh, M.P. Couto, K.H. Ardakani, and C.M. Brown, "Excitation Light Dose Engineering to Reduce Photo-bleaching and Photo-toxicity", Scientific Reports, vol. 6, 2016.
  13. F. Baumgart, A.M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G.J. Schütz, "Varying label density allows artifact-free analysis of membrane-protein nanoclusters", Nature Methods, vol. 13, pp. 661-664, 2016.
  14. M.E. Masip, J. Huebinger, J. Christmann, O. Sabet, F. Wehner, A. Konitsiotis, G.R. Fuhr, and P.I.H. Bastiaens, "Reversible cryo-arrest for imaging molecules in living cells at high spatial resolution", Nature Methods, vol. 13, pp. 665-672, 2016.
  15. A.F. Coskun, and L. Cai, "Dense transcript profiling in single cells by image correlation decoding", Nature Methods, vol. 13, pp. 657-660, 2016.
  16. P. GEORGIADES, V.J. ALLAN, M. DICKINSON, and T.A. WAIGH, "Reduction of coherent artefacts in super-resolution fluorescence localisation microscopy", Journal of Microscopy, vol. 264, pp. 375-383, 2016.
  17. D.M. Shcherbakova, M. Baloban, A.V. Emelyanov, M. Brenowitz, P. Guo, and V.V. Verkhusha, "Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging", Nature Communications, vol. 7, 2016.