Paper Roundup: November 2013

  • A review on determining protein quaternary structure by FRET. I’m a little skeptical of their ability to extract as much information from (typically noisy) FRET data as they want to, but it’s an interesting review nonetheless. [1]
  • Using GFP-labeled TALEs to fluorescently label chromosomal regions [2]
  • Another compressed sensing algorithm for fast STORM/PALM imaging [3]
  • A review on Raman microscopy [4]
  • STED imaging of individual diamond nitrogen vacancies with ~10 nm resolution [5]
  • Ultra-high speed 3D imaging of second harmonic generation using holography [6]
  • Single molecule super-resolution imaging used to count molecules and measure the fraction of dimers [7]
  • High speed 3D holographic imaging of ciliary beating [8]
  • Temperature sensitive GFPs for measurement of the temperature inside cells [9]
  • An improved version of the spinach aptamer, spinach2, for fluorescent labeling of RNAs [10]
  • A new method for monovalent functionalization of quantum dots for single molecule labeling and imaging [11]
  • A new method for segmenting nuclei. It has a nice overview of current algorithms for nuclear segmentation in the introduction [12]
  • A microfluidic method for trapping cells in droplets and imaging them for long periods of time [13]
  • A review of superresolution localization methods, specifically on fitting algorithms [14]
  • An introduction to machine learning approaches for analyzing imaging data in cell biology [15]


  1. V. Raicu, and D. Singh, "FRET Spectrometry: A New Tool for the Determination of Protein Quaternary Structure in Living Cells", Biophysical Journal, vol. 105, pp. 1937-1945, 2013.
  2. Y. Miyanari, C. Ziegler-Birling, and M. Torres-Padilla, "Live visualization of chromatin dynamics with fluorescent TALEs", Nature Structural & Molecular Biology, vol. 20, pp. 1321-1324, 2013.
  3. H.P. Babcock, J.R. Moffitt, Y. Cao, and X. Zhuang, "Fast compressed sensing analysis for super-resolution imaging using L1-homotopy", Optics Express, vol. 21, pp. 28583, 2013.
  4. K.A. Antonio, and Z.D. Schultz, "Advances in Biomedical Raman Microscopy", Analytical Chemistry, vol. 86, pp. 30-46, 2013.
  5. S. Arroyo-Camejo, M. Adam, M. Besbes, J. Hugonin, V. Jacques, J. Greffet, J. Roch, S.W. Hell, and F. Treussart, "Stimulated Emission Depletion Microscopy Resolves Individual Nitrogen Vacancy Centers in Diamond Nanocrystals", ACS Nano, vol. 7, pp. 10912-10919, 2013.
  6. D.R. Smith, D.G. Winters, and R.A. Bartels, "Submillisecond second harmonic holographic imaging of biological specimens in three dimensions", Proceedings of the National Academy of Sciences, vol. 110, pp. 18391-18396, 2013.
  7. X. Nan, E.A. Collisson, S. Lewis, J. Huang, T.M. Tamguney, J.T. Liphardt, F. McCormick, J.W. Gray, and S. Chu, "Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling", Proceedings of the National Academy of Sciences, vol. 110, pp. 18519-18524, 2013.
  8. L.G. Wilson, L.M. Carter, and S.E. Reece, "High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms", Proceedings of the National Academy of Sciences, vol. 110, pp. 18769-18774, 2013.
  9. S. Kiyonaka, T. Kajimoto, R. Sakaguchi, D. Shinmi, M. Omatsu-Kanbe, H. Matsuura, H. Imamura, T. Yoshizaki, I. Hamachi, T. Morii, and Y. Mori, "Genetically encoded fluorescent thermosensors visualize subcellular thermoregulation in living cells", Nature Methods, vol. 10, pp. 1232-1238, 2013.
  10. R.L. Strack, M.D. Disney, and S.R. Jaffrey, "A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA", Nature Methods, vol. 10, pp. 1219-1224, 2013.
  11. J. Farlow, D. Seo, K.E. Broaders, M.J. Taylor, Z.J. Gartner, and Y. Jun, "Formation of targeted monovalent quantum dots by steric exclusion", Nature Methods, vol. 10, pp. 1203-1205, 2013.
  12. J. QI, "Dense nuclei segmentation based on graph cut and convexity-concavity analysis", Journal of Microscopy, vol. 253, pp. 42-53, 2013.
  13. M.A. Khorshidi, P.K.P. Rajeswari, C. Wählby, H.N. Joensson, and H. Andersson Svahn, "Automated analysis of dynamic behavior of single cells in picoliter droplets", Lab on a Chip, vol. 14, pp. 931, 2014.
  14. A.R. Small, and R. Parthasarathy, "Superresolution Localization Methods", Annual Review of Physical Chemistry, vol. 65, pp. 107-125, 2014.
  15. C. Sommer, and D.W. Gerlich, "Machine learning in cell biology – teaching computers to recognize phenotypes", Journal of Cell Science, vol. 126, pp. 5529-5539, 2013.