Paper Roundup – November 2016

  • A detailed investigation of ER structure by multiple super-resolution methods [1]
  • Using deep convolutional neural networks to segment cells automatically with high accuracy [2]
  • A light sheet microscope that automatically adjusts the illumination plane to correct for sample-induced distortion [3]
  • Tools for scanning angle interference microscopy (SAIM) acquisition and analysis [4]
  • Super-resolution mapping of fluorophore orientation [5]
  • Isotropic point spread functions for fast cellular resolution 2-photon imaging [6]
  • CyRFP1, a long Stokes shift fluorescent protein co-excited with GFP but with separable emission [7]
  • mMaroon1, a new far-red fluorescent protein, and a four-color Fucci cell cycle sensor [8]
  • Multi-color electron microscopy [9]
  • A detailed review of fluorescent proteins [10]
  • A nice discussion of challenges in live cell time lapse imaging [11]
  • Ni2+ as a triplet state quencher for improved light output from Cy3 and Cy5 [12]
  • A python tool for image analysis [13]
  • Optimal reconstruction of 2D-SIM data [14]
  • A new bright monomeric red fluorescent protein, mScarlet [15]
  • A review of fluorescent tagging methods [16]
  • Adaptive SIM microscopy to reduce bleaching [17]
  • Tools for cluster analysis of single molecule localization microscopy methods [18]
  • A super-resolution microscope based on incoherent holography [19]


  1. J. Nixon-Abell, C.J. Obara, A.V. Weigel, D. Li, W.R. Legant, C.S. Xu, H.A. Pasolli, K. Harvey, H.F. Hess, E. Betzig, C. Blackstone, and J. Lippincott-Schwartz, "Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER", Science, vol. 354, pp. aaf3928-aaf3928, 2016.
  2. D.A. Van Valen, T. Kudo, K.M. Lane, D.N. Macklin, N.T. Quach, M.M. DeFelice, I. Maayan, Y. Tanouchi, E.A. Ashley, and M.W. Covert, "Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments", PLOS Computational Biology, vol. 12, pp. e1005177, 2016.
  3. L.A. Royer, W.C. Lemon, R.K. Chhetri, Y. Wan, M. Coleman, E.W. Myers, and P.J. Keller, "Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms", Nature Biotechnology, vol. 34, pp. 1267-1278, 2016.
  4. C.B. Carbone, R.D. Vale, and N. Stuurman, "An acquisition and analysis pipeline for scanning angle interference microscopy", Nature Methods, vol. 13, pp. 897-898, 2016.
  5. K. Zhanghao, L. Chen, X. Yang, M. Wang, Z. Jing, H. Han, M.Q. Zhang, D. Jin, J. Gao, and P. Xi, "Super-resolution dipole orientation mapping via polarization demodulation", Light: Science & Applications, vol. 5, pp. e16166-e16166, 2016.
  6. R. Prevedel, A.J. Verhoef, A.J. Pernía-Andrade, S. Weisenburger, B.S. Huang, T. Nöbauer, A. Fernández, J.E. Delcour, P. Golshani, A. Baltuska, and A. Vaziri, "Fast volumetric calcium imaging across multiple cortical layers using sculpted light", Nature Methods, vol. 13, pp. 1021-1028, 2016.
  7. T. Laviv, B.B. Kim, J. Chu, A.J. Lam, M.Z. Lin, and R. Yasuda, "Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins", Nature Methods, vol. 13, pp. 989-992, 2016.
  8. B.T. Bajar, A.J. Lam, R.K. Badiee, Y. Oh, J. Chu, X.X. Zhou, N. Kim, B.B. Kim, M. Chung, A.L. Yablonovitch, B.F. Cruz, K. Kulalert, J.J. Tao, T. Meyer, X. Su, and M.Z. Lin, "Fluorescent indicators for simultaneous reporting of all four cell cycle phases", Nature Methods, vol. 13, pp. 993-996, 2016.
  9. S. Adams, M. Mackey, R. Ramachandra, S. Palida Lemieux, P. Steinbach, E. Bushong, M. Butko, B. Giepmans, M. Ellisman, and R. Tsien, "Multicolor Electron Microscopy for Simultaneous Visualization of Multiple Molecular Species", Cell Chemical Biology, vol. 23, pp. 1417-1427, 2016.
  10. E.A. Rodriguez, R.E. Campbell, J.Y. Lin, M.Z. Lin, A. Miyawaki, A.E. Palmer, X. Shu, J. Zhang, and R.Y. Tsien, "The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins", Trends in Biochemical Sciences, vol. 42, pp. 111-129, 2017.
  11. S. Skylaki, O. Hilsenbeck, and T. Schroeder, "Challenges in long-term imaging and quantification of single-cell dynamics", Nature Biotechnology, vol. 34, pp. 1137-1144, 2016.
  12. V. Glembockyte, J. Lin, and G. Cosa, "Improving the Photostability of Red- and Green-Emissive Single-Molecule Fluorophores via Ni2+Mediated Excited Triplet-State Quenching", The Journal of Physical Chemistry B, vol. 120, pp. 11923-11929, 2016.
  13. T.S.G. Olsson, and M. Hartley, "jicbioimage: a tool for automated and reproducible bioimage analysis", PeerJ, vol. 4, pp. e2674, 2016.
  14. V. Perez, B. Chang, and E.H.K. Stelzer, "Optimal 2D-SIM reconstruction by two filtering steps with Richardson-Lucy deconvolution", Scientific Reports, vol. 6, 2016.
  15. D.S. Bindels, L. Haarbosch, L. van Weeren, M. Postma, K.E. Wiese, M. Mastop, S. Aumonier, G. Gotthard, A. Royant, M.A. Hink, and T.W.J. Gadella, "mScarlet: a bright monomeric red fluorescent protein for cellular imaging", Nature Methods, vol. 14, pp. 53-56, 2016.
  16. E.A. Specht, E. Braselmann, and A.E. Palmer, "A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging", Annual Review of Physiology, vol. 79, pp. 93-117, 2017.
  17. N. Chakrova, A.S. Canton, C. Danelon, S. Stallinga, and B. Rieger, "Adaptive illumination reduces photobleaching in structured illumination microscopy", Biomedical Optics Express, vol. 7, pp. 4263, 2016.
  18. J. Griffié, M. Shannon, C.L. Bromley, L. Boelen, G.L. Burn, D.J. Williamson, N.A. Heard, A.P. Cope, D.M. Owen, and P. Rubin-Delanchy, "A Bayesian cluster analysis method for single-molecule localization microscopy data", Nature Protocols, vol. 11, pp. 2499-2514, 2016.
  19. N. Siegel, V. Lupashin, B. Storrie, and G. Brooker, "High-magnification super-resolution FINCH microscopy using birefringent crystal lens interferometers", Nature Photonics, vol. 10, pp. 802-808, 2016.