Paper Roundup – October 2014

  • PSFj is a new tool to automatically measure point spread functions and report the performance of your microscope across the field of view. It looks promising, although I would love a similar tool that not only measured PSF size but also could fit a set of Zernike polynomials to evaluate astigmatishm, spherical aberration, etc. [1]
  • FEBS Letters has a special issue on single molecule approaches, including in vivo single molecule imaging.
  • There is a nice introduction to fluorescence and confocal microscopy in CSH Protocols [2]
  • An improved method for wavefront correction in the two-photon microscope for correcting sample-induced aberrations in deep imaging [3]
  • Single molecule imaging in living cells using 24 repeats of a peptide sequence fused to the protein of interest that is then bound by a coexpressed scFv [4]
  • Combinations of fluorescent proteins for 2-photon imaging [5]
  • Generation of long light sheets by scanning the focus of a gaussian beam using a acoustically tunable lens [6]
  • An improved system for localization microscopy using both astigmatism and biplane imaging [7]
  • The Betzig group has put together another technical tour-de-force – a lattice light sheet microscope capable of high resolution 3D imaging over long periods of time [8]
  • Plans for an open-hardware two-photo system using Thorlabs parts for the optomechanics [9]
  • Computational evolution of a resorufin ligase to covalently attach resorufin to a small, 13-aa tag [10]
  • A protocol describing assembly and alignment of the diSPIM system [11]
  • A high speed 3D imaging system using remote focusing and structured illumination [12]
  • A brighter green fluorescent RNA aptamer that binds DHFBI, Broccoli [13]
  • Using a fluorogen-activating protein for single particle tracking where particle density can be titrated by controlling the level of the fluorogen [14]


  1. P. Theer, C. Mongis, and M. Knop, "PSFj: know your fluorescence microscope", Nature Methods, vol. 11, pp. 981-982, 2014.
  2. M.J. Sanderson, I. Smith, I. Parker, and M.D. Bootman, "Fluorescence Microscopy", Cold Spring Harbor Protocols, vol. 2014, pp. pdb.top071795-pdb.top071795, 2014.
  3. C. Wang, R. Liu, D.E. Milkie, W. Sun, Z. Tan, A. Kerlin, T. Chen, D.S. Kim, and N. Ji, "Multiplexed aberration measurement for deep tissue imaging in vivo", Nature Methods, vol. 11, pp. 1037-1040, 2014.
  4. M. Tanenbaum, L. Gilbert, L. Qi, J. Weissman, and R. Vale, "A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging", Cell, vol. 159, pp. 635-646, 2014.
  5. S. Gossa, D. Nayak, B.H. Zinselmeyer, and D.B. McGavern, "Development of an Immunologically Tolerated Combination of Fluorescent Proteins for In vivo Two-photon Imaging", Scientific Reports, vol. 4, 2014.
  6. K.M. Dean, and R. Fiolka, "Uniform and scalable light-sheets generated by extended focusing", Optics Express, vol. 22, pp. 26141, 2014.
  7. J. Min, S.J. Holden, L. Carlini, M. Unser, S. Manley, and J.C. Ye, "3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction", Biomedical Optics Express, vol. 5, pp. 3935, 2014.
  8. B. Chen, W.R. Legant, K. Wang, L. Shao, D.E. Milkie, M.W. Davidson, C. Janetopoulos, X.S. Wu, J.A. Hammer, Z. Liu, B.P. English, Y. Mimori-Kiyosue, D.P. Romero, A.T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R.D. Mullins, D.M. Mitchell, J.N. Bembenek, A. Reymann, R. Böhme, S.W. Grill, J.T. Wang, G. Seydoux, U.S. Tulu, D.P. Kiehart, and E. Betzig, "Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution", Science, vol. 346, pp. 1257998, 2014.
  9. D.G. Rosenegger, C.H.T. Tran, J. LeDue, N. Zhou, and G.R. Gordon, "A High Performance, Cost-Effective, Open-Source Microscope for Scanning Two-Photon Microscopy that Is Modular and Readily Adaptable", PLoS ONE, vol. 9, pp. e110475, 2014.
  10. D.S. Liu, L.G. Nivon, F. Richter, P.J. Goldman, T.J. Deerinck, J.Z. Yao, D. Richardson, W.S. Phipps, A.Z. Ye, M.H. Ellisman, C.L. Drennan, D. Baker, and A.Y. Ting, "Computational design of a red fluorophore ligase for site-specific protein labeling in living cells", Proceedings of the National Academy of Sciences, vol. 111, pp. E4551-E4559, 2014.
  11. A. Kumar, Y. Wu, R. Christensen, P. Chandris, W. Gandler, E. McCreedy, A. Bokinsky, D.A. Colón-Ramos, Z. Bao, M. McAuliffe, G. Rondeau, and H. Shroff, "Dual-view plane illumination microscopy for rapid and spatially isotropic imaging", Nature Protocols, vol. 9, pp. 2555-2573, 2014.
  12. H. Choi, D.N. Wadduwage, T.Y. Tu, P. Matsudaira, and P.T.C. So, "Three-dimensional image cytometer based on widefield structured light microscopy and high-speed remote depth scanning", Cytometry Part A, vol. 87, pp. 49-60, 2014.
  13. G.S. Filonov, J.D. Moon, N. Svensen, and S.R. Jaffrey, "Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution", Journal of the American Chemical Society, vol. 136, pp. 16299-16308, 2014.
  14. S.L. Schwartz, Q. Yan, C.A. Telmer, K.A. Lidke, M.P. Bruchez, and D.S. Lidke, "Fluorogen-Activating Proteins Provide Tunable Labeling Densities for Tracking FcεRI Independent of IgE", ACS Chemical Biology, vol. 10, pp. 539-546, 2014.

One thought on “Paper Roundup – October 2014

  1. Dear Kurt,

    It has been a great pleasure to read your blog. Here I’d like to add a paper we published about using similar tunable acoustic lens to generate a two-photon lightsheet microscope. We have reported our finding this June at CLEO (, and the full paper is out in Cell Research in September ( The method takes full advantage of thin sheet and deep penetration.



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