Paper Roundup – April 2014

  • A new buffer system for stabilizing single molecule fluorescence and preventing blinking and bleaching using a redox system combined with a thiol. [1]
  • A paper characterizing small carbon dots as fluorescent reporters. Interestingly they can be excited at multiple different wavelengths, giving rise to different emission spectra. [2]
  • Bright upconverting nanoparticles for single molecule imaging. [3]
  • A review of environmentally sensitive small molecule dyes. [4]
  • A review of fluorescence fluctuation approaches, such as image correlation spectroscopy. [5]
  • A two photon version of multifocal SIM for super-resolution imaging in thick tissues. [6]
  • A review of and protocol for constructing a Bessel-beam light-sheet system. [7]
  • An advanced compressed sensing approach to reconstructing localization microscopy data [8]
  • A protocol for intensity calibration and flat-field correction for fluorescence microscopes [9]
  • A low-cost single color localization microscopy system using a single diode laser and an arc lamp for activation [10]
  • A new algorithm for structured illumination reconstruction at low light levels [11]
  • Optimized scan and tube lenses for confocal microscopes [12]
  • A DMD-based multi-angle TIRF illuminator [13]
  • A FRET sensor for abscisic acid in plants; the interesting thing about this paper is the systematic optimization of the FRET biosensor by testing multiple fluorescent proteins and linkers. [14]
  • A novel point-spread function engineering approach for isotropic 3D localization of single molecules over large thicknesses [15]
  • A very impressive adaptive optics confocal system from the Betzig group. It uses a two-photon excited guide star to correct the wavefront across large scan areas and enables diffraction limited one-photon confocal imaging to 200 μm deep. [16]
  • Stimulated Raman scattering imaging of alkyne-labeled molecules in live cells [17]
  • Rotating polarization excitation and polarization dependent stimulated depletion used to generate super-resolution images in widefield microscopy [18]
  • Single molecule imaging in C. elegans using near-TIRF imaging and GFP RNAi to reduce the expression level, combined with an analysis of replacement of photobleached GFPs to infer transport kinetics. [19]
  • A good review on labeling and imaging methods for whole-embryo imaging [20]
  • A new brain clearing procedure for imaging whole mouse brains [21]
  • Multiview deconvolution for fusing light sheet images taken from different direction [22]
  • A simple, lens-free, holographic imaging system for imaging cell migration over large fields of view [23]
  • A note about the (in)applicability of structured illumination to coherent imaging [24]
  • An Airy beam light sheet microscope [25]
  • ThunderSTORM, an ImageJ plugin for analysis and simulation of 2D/3D localization microscopy data (code and plugin here) [26]


  1. P. Holzmeister, A. Gietl, and P. Tinnefeld, "Geminate Recombination as a Photoprotection Mechanism for Fluorescent Dyes", Angewandte Chemie International Edition, vol. 53, pp. 5685-5688, 2014.
  2. G.E. LeCroy, S.K. Sonkar, F. Yang, L.M. Veca, P. Wang, K.N. Tackett, J. Yu, E. Vasile, H. Qian, Y. Liu, P.(. Luo, and Y. Sun, "Toward Structurally Defined Carbon Dots as Ultracompact Fluorescent Probes", ACS Nano, vol. 8, pp. 4522-4529, 2014.
  3. D.J. Gargas, E.M. Chan, A.D. Ostrowski, S. Aloni, M.V.P. Altoe, E.S. Barnard, B. Sanii, J.J. Urban, D.J. Milliron, B.E. Cohen, and P.J. Schuck, "Engineering bright sub-10-nm upconverting nanocrystals for single-molecule imaging", Nature Nanotechnology, vol. 9, pp. 300-305, 2014.
  4. Z. Yang, J. Cao, Y. He, J.H. Yang, T. Kim, X. Peng, and J.S. Kim, "Macro-/micro-environment-sensitive chemosensing and biological imaging", Chem. Soc. Rev., vol. 43, pp. 4563-4601, 2014.
  5. N. Bag, and T. Wohland, "Imaging Fluorescence Fluctuation Spectroscopy: New Tools for Quantitative Bioimaging", Annual Review of Physical Chemistry, vol. 65, pp. 225-248, 2014.
  6. M. Ingaramo, A.G. York, P. Wawrzusin, O. Milberg, A. Hong, R. Weigert, H. Shroff, and G.H. Patterson, "Two-photon excitation improves multifocal structured illumination microscopy in thick scattering tissue", Proceedings of the National Academy of Sciences, vol. 111, pp. 5254-5259, 2014.
  7. L. Gao, L. Shao, B. Chen, and E. Betzig, "3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy", Nature Protocols, vol. 9, pp. 1083-1101, 2014.
  8. J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J.C. Ye, and M. Unser, "FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data", Scientific Reports, vol. 4, 2014.
  9. M. Model, "Intensity Calibration and Flat-Field Correction for Fluorescence Microscopes", Current Protocols in Cytometry, vol. 68, pp. 10.14.1-10.14.10, 2014.
  10. Z. Yuan, J. Sun, R. Zhai, X. Li, and Z. Shao, "Mercury arc lamp based super-resolution imaging with conventional fluorescence microscopes", Micron, vol. 59, pp. 24-27, 2014.
  11. K. Chu, P.J. McMillan, Z.J. Smith, J. Yin, J. Atkins, P. Goodwin, S. Wachsmann-Hogiu, and S. Lane, "Image reconstruction for structured-illumination microscopy with low signal level", Optics Express, vol. 22, pp. 8687, 2014.
  12. A. Negrean, and H.D. Mansvelder, "Optimal lens design and use in laser-scanning microscopy", Biomedical Optics Express, vol. 5, pp. 1588, 2014.
  13. W. Zong, X. Huang, C. Zhang, T. Yuan, L. Zhu, M. Fan, and L. Chen, "Shadowless-illuminated variable-angle TIRF (siva-TIRF) microscopy for the observation of spatial-temporal dynamics in live cells", Biomedical Optics Express, vol. 5, pp. 1530, 2014.
  14. A.M. Jones, J.. Danielson, S.N. ManojKumar, V. Lanquar, G. Grossmann, and W.B. Frommer, "Abscisic acid dynamics in roots detected with genetically encoded FRET sensors", eLife, vol. 3, 2014.
  15. S. Jia, J.C. Vaughan, and X. Zhuang, "Isotropic three-dimensional super-resolution imaging with a self-bending point spread function", Nature Photonics, vol. 8, pp. 302-306, 2014.
  16. K. Wang, D.E. Milkie, A. Saxena, P. Engerer, T. Misgeld, M.E. Bronner, J. Mumm, and E. Betzig, "Rapid adaptive optical recovery of optimal resolution over large volumes", Nature Methods, vol. 11, pp. 625-628, 2014.
  17. L. Wei, F. Hu, Y. Shen, Z. Chen, Y. Yu, C. Lin, M.C. Wang, and W. Min, "Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering", Nature Methods, vol. 11, pp. 410-412, 2014.
  18. N. Hafi, M. Grunwald, L.S. van den Heuvel, T. Aspelmeier, J. Chen, M. Zagrebelsky, O.M. Schütte, C. Steinem, M. Korte, A. Munk, and P.J. Walla, "Fluorescence nanoscopy by polarization modulation and polarization angle narrowing", Nature Methods, vol. 11, pp. 579-584, 2014.
  19. F.B. Robin, W.M. McFadden, B. Yao, and E.M. Munro, "Single-molecule analysis of cell surface dynamics in Caenorhabditis elegans embryos", Nature Methods, vol. 11, pp. 677-682, 2014.
  20. P. Pantazis, and W. Supatto, "Advances in whole-embryo imaging: a quantitative transition is underway", Nature Reviews Molecular Cell Biology, vol. 15, pp. 327-339, 2014.
  21. E. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. Ueda, "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis", Cell, vol. 157, pp. 726-739, 2014.
  22. S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R.H. Singer, E. Myers, and P. Tomancak, "Efficient Bayesian-based multiview deconvolution", Nature Methods, vol. 11, pp. 645-648, 2014.
  23. I. Pushkarsky, Y. Liu, W. Weaver, T. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, "Automated single-cell motility analysis on a chip using lensfree microscopy", Scientific Reports, vol. 4, 2014.
  24. K. Wicker, and R. Heintzmann, "Resolving a misconception about structured illumination", Nature Photonics, vol. 8, pp. 342-344, 2014.
  25. T. Vettenburg, H.I.C. Dalgarno, J. Nylk, C. Coll-Lladó, D.E.K. Ferrier, T. Čižmár, F.J. Gunn-Moore, and K. Dholakia, "Light-sheet microscopy using an Airy beam", Nature Methods, vol. 11, pp. 541-544, 2014.
  26. M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G.M. Hagen, "ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging", Bioinformatics, vol. 30, pp. 2389-2390, 2014.