Paper Roundup – March 2014

  • An automated computational approach for recognizing cell phenotypes from images [1]. Nicely, they make their source code open source.
  • A spinning TIRF system with polarization control, so that constant illumination polarization is maintained at the sample while the beam rotates around the back aperture [2]
  • A pair of papers on identifying and removing the background scattered light in TIRF imaging which gives rise to non-TIRF background fluorescence. [3][4], and a commentary on it [5]
  • Lavis and Raines have a new review out on the chemistry of fluorophores, focusing on the synthesis and application of common fluorophore scaffolds. [6]
  • Calculations of expected FRET signals from non-interacting proteins in the membrane. Important for separating ‘bystander’ FRET from FRET due to true protein interaction. [7][8]
  • A head-to-head competition of particle-tracking algorithms: article [9] and commentary [10].
  • A detailed protocol for generating and testing monomeric fluorescent proteins. [11]
  • A low-cost, homebuilt motorized microscope stage [12]
  • mCardinal – an intrinisically fluorescent protein that is the brightest protein to date for imaging in the far-red (~Cy5) region. [13]
  • ChemPhysChem has an issue focused on super-resolution imaging, including articles on localization imaging using stochastic binding of dyes to fluorogen activating proteins [14], a review on combining single molecule super resolution imaging and light sheet microscopy [15], and a review of structured illumination microscopy [16]
  • An image-based assay using five fluorescent channels and six stains to extract seven cellular components. The paper includes detailed protocols and the CellProfiler pipelines used to analyze the data. [17]
  • Using fluorescent protein – TALE fusions to mark satellite sequences in Drosophila [18]
  • A low cost microscope built from Thorlabs parts for neuroscience imaging [19]
  • High-throughput PALM imaging of bacteria [20]


  1. S. Basu, S. Kolouri, and G.K. Rohde, "Detecting and visualizing cell phenotype differences from microscopy images using transport-based morphometry", Proceedings of the National Academy of Sciences, vol. 111, pp. 3448-3453, 2014.
  2. D. Johnson, R. Toledo-Crow, A. Mattheyses, and S. Simon, "Polarization-Controlled TIRFM with Focal Drift and Spatial Field Intensity Correction", Biophysical Journal, vol. 106, pp. 1008-1019, 2014.
  3. M. Brunstein, M. Teremetz, K. Hérault, C. Tourain, and M. Oheim, "Eliminating Unwanted Far-Field Excitation in Objective-Type TIRF. Part I. Identifying Sources of Nonevanescent Excitation Light", Biophysical Journal, vol. 106, pp. 1020-1032, 2014.
  4. M. Brunstein, K. Hérault, and M. Oheim, "Eliminating Unwanted Far-Field Excitation in Objective-Type TIRF. Part II. Combined Evanescent-Wave Excitation and Supercritical-Angle Fluorescence Detection Improves Optical Sectioning", Biophysical Journal, vol. 106, pp. 1044-1056, 2014.
  5. C. Yip, "Star Light, Star Bright, First Molecule I See Tonight", Biophysical Journal, vol. 106, pp. 987-988, 2014.
  6. L.D. Lavis, and R.T. Raines, "Bright Building Blocks for Chemical Biology", ACS Chemical Biology, vol. 9, pp. 855-866, 2014.
  7. C. King, S. Sarabipour, P. Byrne, D. Leahy, and K. Hristova, "The FRET Signatures of Noninteracting Proteins in Membranes: Simulations and Experiments", Biophysical Journal, vol. 106, pp. 1309-1317, 2014.
  8. A. Clayton, and A. Chattopadhyay, "Taking Care of Bystander FRET in a Crowded Cell Membrane Environment", Biophysical Journal, vol. 106, pp. 1227-1228, 2014.
  9. N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I.F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A.R. Cohen, W.J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K.E.G. Magnusson, J. Jaldén, H.M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Tinevez, S.L. Shorte, J. Willemse, K. Celler, G.P. van Wezel, H. Dan, Y. Tsai, C.O. de Solórzano, J. Olivo-Marin, and E. Meijering, "Objective comparison of particle tracking methods", Nature Methods, vol. 11, pp. 281-289, 2014.
  10. M.J. Saxton, "A particle tracking meet", Nature Methods, vol. 11, pp. 247-248, 2014.
  11. H. Ai, M.A. Baird, Y. Shen, M.W. Davidson, and R.E. Campbell, "Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications", Nature Protocols, vol. 9, pp. 910-928, 2014.
  12. R.A.A. Campbell, R.W. Eifert, and G.C. Turner, "Openstage: A Low-Cost Motorized Microscope Stage with Sub-Micron Positioning Accuracy", PLoS ONE, vol. 9, pp. e88977, 2014.
  13. J. Chu, R.D. Haynes, S.Y. Corbel, P. Li, E. González-González, J.S. Burg, N.J. Ataie, A.J. Lam, P.J. Cranfill, M.A. Baird, M.W. Davidson, H. Ng, K.C. Garcia, C.H. Contag, K. Shen, H.M. Blau, and M.Z. Lin, "Non-invasive intravital imaging of cellular differentiation with a bright red-excitable fluorescent protein", Nature Methods, vol. 11, pp. 572-578, 2014.
  14. Q. Yan, S.L. Schwartz, S. Maji, F. Huang, C. Szent-Gyorgyi, D.S. Lidke, K.A. Lidke, and M.P. Bruchez, "Localization Microscopy using Noncovalent Fluorogen Activation by Genetically Encoded Fluorogen-Activating Proteins.", ChemPhysChem, vol. 15, pp. 687-695, 2013.
  15. Y.S. Hu, M. Zimmerley, Y. Li, R. Watters, and H. Cang, "Single-Molecule Super-Resolution Light-Sheet Microscopy", ChemPhysChem, vol. 15, pp. 577-586, 2014.
  16. J.R. Allen, S.T. Ross, and M.W. Davidson, "Structured Illumination Microscopy for Superresolution", ChemPhysChem, vol. 15, pp. 566-576, 2014.
  17. S.M. Gustafsdottir, V. Ljosa, K.L. Sokolnicki, J. Anthony Wilson, D. Walpita, M.M. Kemp, K. Petri Seiler, H.A. Carrel, T.R. Golub, S.L. Schreiber, P.A. Clemons, A.E. Carpenter, and A.F. Shamji, "Multiplex Cytological Profiling Assay to Measure Diverse Cellular States", PLoS ONE, vol. 8, pp. e80999, 2013.
  18. K. Yuan, A.W. Shermoen, and P.H. O’Farrell, "Illuminating DNA replication during Drosophila development using TALE-lights", Current Biology, vol. 24, pp. R144-R145, 2014.
  19. L. Beltran-Parrazal, C. Morgado-Valle, R.E. Serrano, J. Manzo, and J.L. Vergara, "Design and construction of a modular low-cost epifluorescence upright microscope for neuron visualized recording and fluorescence detection", Journal of Neuroscience Methods, vol. 225, pp. 57-64, 2014.
  20. S.J. Holden, T. Pengo, K.L. Meibom, C. Fernandez Fernandez, J. Collier, and S. Manley, "High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization", Proceedings of the National Academy of Sciences, vol. 111, pp. 4566-4571, 2014.