Paper Roundup – May 2015

  • MorphoGraphX – an open source program for segmentation and analysis of 3D data [1]
  • This is an EM paper, but something I’ve always wanted to see: a method to tag proteins for visualization in EM with a metal binding protein [2]
  • A capillary-based sample holder that allows rotation of a sample through 360 degrees while being imaged [3]
  • Adaptive optics for spinning disk confocal microscopy [4]
  • Optimized fluorogen activating proteins for fluorescent labeling with malachite green ester [5]
  • Micro-mirrors for single objective light sheet imaging [6]
  • A review of open-source tools for neuroscience, much of which is focused on image processing [7]
  • Using an electrically tunable lens for rapidly moving the focal plane of a two-photon microscope [8]
  • A proximity ligation approach for visualizing newly synthesized proteins of interest [9]
  • A post hoc method for flat-fielding of microscopy data [10]
  • Multfocus microscopy for single molecule tracking of diffusing RNAs [11]
  • A ribityl-lumazine binding protein with a very long (13.6 ns) fluorescence lifetime for FRET and anisotropy measurements [12]
  • Riboswitches for fluorescence imaging of metabolites using the Spinach aptamer [13]
  • Optimizing imaging frame rate and laser power for localization microscopy of Alexa647 [14]
  • Electrophoretically driven antibody labeling of hydrogel-embedded tissues [15]
  • Intelligent acquisition software for Leica microscopes [16]
  • A review of novel fluorescent protein developments [17]


  1. "Abstract", .
  2. M. MORPHEW, E. O'TOOLE, C. PAGE, M. PAGRATIS, J. MEEHL, T. GIDDINGS, J. GARDNER, C. ACKERSON, S. JASPERSEN, M. WINEY, A. HOENGER, and J. MCINTOSH, "Metallothionein as a clonable tag for protein localization by electron microscopy of cells", Journal of Microscopy, vol. 260, pp. 20-29, 2015.
  3. T. BRUNS, S. SCHICKINGER, and H. SCHNECKENBURGER, "Sample holder for axial rotation of specimens in 3D microscopy", Journal of Microscopy, vol. 260, pp. 30-36, 2015.
  4. V. FRAISIER, G. CLOUVEL, A. JASAITIS, A. DIMITROV, T. PIOLOT, and J. SALAMERO, "Adaptive optics in spinning disk microscopy: improved contrast and brightness by a simple and fast method", Journal of Microscopy, vol. 259, pp. 219-227, 2015.
  5. C.A. Telmer, R. Verma, H. Teng, S. Andreko, L. Law, and M.P. Bruchez, "Rapid, Specific, No-wash, Far-red Fluorogen Activation in Subcellular Compartments by Targeted Fluorogen Activating Proteins", ACS Chemical Biology, vol. 10, pp. 1239-1246, 2015.
  6. R. Galland, G. Grenci, A. Aravind, V. Viasnoff, V. Studer, and J. Sibarita, "3D high- and super-resolution imaging using single-objective SPIM", Nature Methods, vol. 12, pp. 641-644, 2015.
  7. J. Freeman, "Open source tools for large-scale neuroscience", Current Opinion in Neurobiology, vol. 32, pp. 156-163, 2015.
  8. P. Annibale, A. Dvornikov, and E. Gratton, "Electrically tunable lens speeds up 3D orbital tracking", Biomedical Optics Express, vol. 6, pp. 2181, 2015.
  9. S. tom Dieck, L. Kochen, C. Hanus, M. Heumüller, I. Bartnik, B. Nassim-Assir, K. Merk, T. Mosler, S. Garg, S. Bunse, D.A. Tirrell, and E.M. Schuman, "Direct visualization of newly synthesized target proteins in situ", Nature Methods, vol. 12, pp. 411-414, 2015.
  10. K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, "CIDRE: an illumination-correction method for optical microscopy", Nature Methods, vol. 12, pp. 404-406, 2015.
  11. C.S. Smith, S. Preibisch, A. Joseph, S. Abrahamsson, B. Rieger, E. Myers, R.H. Singer, and D. Grunwald, "Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking", Journal of Cell Biology, vol. 209, pp. 609-619, 2015.
  12. A.C. Hoepker, A. Wang, A. Le Marois, K. Suhling, Y. Yan, and G. Marriott, "Genetically encoded sensors of protein hydrodynamics and molecular proximity", Proceedings of the National Academy of Sciences, vol. 112, pp. E2569-E2574, 2015.
  13. M. You, J.L. Litke, and S.R. Jaffrey, "Imaging metabolite dynamics in living cells using a Spinach-based riboswitch", Proceedings of the National Academy of Sciences, vol. 112, pp. E2756-E2765, 2015.
  14. Y. Lin, J.J. Long, F. Huang, W.C. Duim, S. Kirschbaum, Y. Zhang, L.K. Schroeder, A.A. Rebane, M.G.M. Velasco, A. Virrueta, D.W. Moonan, J. Jiao, S.Y. Hernandez, Y. Zhang, and J. Bewersdorf, "Quantifying and Optimizing Single-Molecule Switching Nanoscopy at High Speeds", PLOS ONE, vol. 10, pp. e0128135, 2015.
  15. J. Li, D.M. Czajkowsky, X. Li, and Z. Shao, "Fast immuno-labeling by electrophoretically driven infiltration for intact tissue imaging", Scientific Reports, vol. 5, 2015.
  16. A. Carro, M. Perez-Martinez, J. Soriano, D.G. Pisano, and D. Megias, "iMSRC: converting a standard automated microscope into an intelligent screening platform", Scientific Reports, vol. 5, 2015.
  17. A.S. Mishin, V.V. Belousov, K.M. Solntsev, and K.A. Lukyanov, "Novel uses of fluorescent proteins", Current Opinion in Chemical Biology, vol. 27, pp. 1-9, 2015.