Paper Roundup – March 2015

  • A spinning-disk confocal based super-resolution system, giving a fast 2-fold improvement in resolution [1]
  • PALMsiever: a localization microscopy tool implementing a number of algorithms for drift correction, clustering, and rendering of localization microscopy data [2]
  • An image-based microfluidic screen for cell deformation [3]
  • Six-color imaging using narrow-band filter sets [4]
  • 3D particle tracking using phase-contrast holography [5]
  • A new super-resolution approach, analogous to STED, that uses a transiently activated quencher dye, whose absorption and quenching is light-dependent [6]
  • A protease reporter based on conversion of iFP from a non-fluorescent to a fluorescent state on protease cleavage [7]
  • Osmium tetroxide fixable mEos4 proteins for correlative super-resolution microscopy and EM [8]
  • A simple chemical modification of many common dyes dramatically improves their quantum yield [9]
  • Ratiometric biosensors by dimeric partner exchange [10]
  • A simplified CLARITY protocol for brain imaging [11]
  • Following translation of RNA by removal of a bound fluorescent protein by the translating ribosome [12]
  • Single molecule imaging of DNA-bound proteins by using energy transfer from a DNA intercalating dye to activate a fluorescent label on a protein bound to the DNA [13]
  • Multicolor CRISPR labeling of chromosomal loci [14]
  • Make your own gridded coverslips using electron beam deposition of metal [15]


  1. S. Hayashi, and Y. Okada, "Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics", Molecular Biology of the Cell, vol. 26, pp. 1743-1751, 2015.
  2. T. Pengo, S.J. Holden, and S. Manley, "PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy", Bioinformatics, vol. 31, pp. 797-798, 2014.
  3. O. Otto, P. Rosendahl, A. Mietke, S. Golfier, C. Herold, D. Klaue, S. Girardo, S. Pagliara, A. Ekpenyong, A. Jacobi, M. Wobus, N. Töpfner, U.F. Keyser, J. Mansfeld, E. Fischer-Friedrich, and J. Guck, "Real-time deformability cytometry: on-the-fly cell mechanical phenotyping", Nature Methods, vol. 12, pp. 199-202, 2015.
  4. S. Kijani, U. Yrlid, M. Heyden, M. Levin, J. Borén, and P. Fogelstrand, "Filter-Dense Multicolor Microscopy", PLOS ONE, vol. 10, pp. e0119499, 2015.
  5. F. Cheong, C. Wong, Y. Gao, M. Nai, Y. Cui, S. Park, L. Kenney, and C. Lim, "Rapid, High-Throughput Tracking of Bacterial Motility in 3D via Phase-Contrast Holographic Video Microscopy", Biophysical Journal, vol. 108, pp. 1248-1256, 2015.
  6. T. Rosales, D.L. Sackett, J. Xu, Z. Shi, B. Xu, H. Li, G. Kaur, E. Frohart, N. Shenoy, S.M. Cheal, H. Wu, A.E. Dulcey, Y. Hu, C. Li, K. Lane, G.L. Griffiths, and J.R. Knutson, "STAQ: A route toward low power, Multicolor nanoscopy", Microscopy Research and Technique, vol. 78, pp. 343-355, 2015.
  7. T. To, B.J. Piggott, K. Makhijani, D. Yu, Y.N. Jan, and X. Shu, "Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo", Proceedings of the National Academy of Sciences, vol. 112, pp. 3338-3343, 2015.
  8. M.G. Paez-Segala, M.G. Sun, G. Shtengel, S. Viswanathan, M.A. Baird, J.J. Macklin, R. Patel, J.R. Allen, E.S. Howe, G. Piszczek, H.F. Hess, M.W. Davidson, Y. Wang, and L.L. Looger, "Fixation-resistant photoactivatable fluorescent proteins for CLEM", Nature Methods, vol. 12, pp. 215-218, 2015.
  9. J.B. Grimm, B.P. English, J. Chen, J.P. Slaughter, Z. Zhang, A. Revyakin, R. Patel, J.J. Macklin, D. Normanno, R.H. Singer, T. Lionnet, and L.D. Lavis, "A general method to improve fluorophores for live-cell and single-molecule microscopy", Nature Methods, vol. 12, pp. 244-250, 2015.
  10. Y. Ding, J. Li, J.R. Enterina, Y. Shen, I. Zhang, P.H. Tewson, G.C.H. Mo, J. Zhang, A.M. Quinn, T.E. Hughes, D. Maysinger, S.C. Alford, Y. Zhang, and R.E. Campbell, "Ratiometric biosensors based on dimerization-dependent fluorescent protein exchange", Nature Methods, vol. 12, pp. 195-198, 2015.
  11. H. Zheng, and L. Rinaman, "Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain", Brain Structure and Function, vol. 221, pp. 2375-2383, 2015.
  12. J.M. Halstead, T. Lionnet, J.H. Wilbertz, F. Wippich, A. Ephrussi, R.H. Singer, and J.A. Chao, "An RNA biosensor for imaging the first round of translation from single cells to living animals", Science, vol. 347, pp. 1367-1671, 2015.
  13. H. Geertsema, A. Schulte, L. Spenkelink, W. McGrath, S. Morrone, J. Sohn, W. Mangel, A. Robinson, and A. van Oijen, "Single-Molecule Imaging at High Fluorophore Concentrations by Local Activation of Dye", Biophysical Journal, vol. 108, pp. 949-956, 2015.
  14. H. Ma, A. Naseri, P. Reyes-Gutierrez, S.A. Wolfe, S. Zhang, and T. Pederson, "Multicolor CRISPR labeling of chromosomal loci in human cells", Proceedings of the National Academy of Sciences, vol. 112, pp. 3002-3007, 2015.
  15. L. Benedetti, E. Sogne, S. Rodighiero, D. Marchesi, P. Milani, and M. Francolini, "Customized patterned substrates for highly versatile correlative light-scanning electron microscopy", Scientific Reports, vol. 4, pp. 7033, 2014.

Online Microscopy Courses

I haven’t been posting much here lately – I’ve been busy with getting my lab up and running and busy with a number of other responsibilities at work. One of the many things I’m doing is putting together a graduate course on microscopy for students at UCSF, which led me to look at what online microscopy and optics courses are out there.  There’s a couple nice ones, which I’ve compiled on the NIC wiki.  If you know of others, please let me know in the comments.

Paper Roundup – February 2015

  • 2,2′-Thiodiethanol as a simple, rapid clearing agent for mouse brains [1]
  • All-optical neurobiology, with optogenetic stimulation and calcium imaging [2]
  • Cell-cycle staging of cell using integrated DNA fluorescence intensity [3]
  • Swept confocally-aligned planar excitation (SCAPE) microscopy, a high-speed light-sheet-like microscopy system for volumetric imaging [4]
  • Some biological applications of STORM imaging: development of the periodic organization of spectrin in neurons [5] and organization of the synaptonemal complex [6]
  • Modifications of the Nikon C1 and C2 confocal scan heads for UV, multiphoton, and FLIM imaging [7]
  • Two new GFPs, hybrids of GFPγ, superfolder GFP, and Clover, with improved brightness and photostability, for yeast tagging [8]


  1. Y. Aoyagi, R. Kawakami, H. Osanai, T. Hibi, and T. Nemoto, "A Rapid Optical Clearing Protocol Using 2,2′-Thiodiethanol for Microscopic Observation of Fixed Mouse Brain", PLOS ONE, vol. 10, pp. e0116280, 2015.
  2. A.M. Packer, L.E. Russell, H.W.P. Dalgleish, and M. Häusser, "Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo", Nature Methods, vol. 12, pp. 140-146, 2014.
  3. V. Roukos, G. Pegoraro, T.C. Voss, and T. Misteli, "Cell cycle staging of individual cells by fluorescence microscopy", Nature Protocols, vol. 10, pp. 334-348, 2015.
  4. M.B. Bouchard, V. Voleti, C.S. Mendes, C. Lacefield, W.B. Grueber, R.S. Mann, R.M. Bruno, and E.M.C. Hillman, "Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms", Nature Photonics, vol. 9, pp. 113-119, 2015.
  5. G. Zhong, J. He, R. Zhou, D. Lorenzo, H.P. Babcock, V. Bennett, and X. Zhuang, "Developmental mechanism of the periodic membrane skeleton in axons", eLife, vol. 3, 2014.
  6. K. Schücker, T. Holm, C. Franke, M. Sauer, and R. Benavente, "Elucidation of synaptonemal complex organization by super-resolution imaging with isotropic resolution", Proceedings of the National Academy of Sciences, vol. 112, pp. 2029-2033, 2015.
  7. S.W. BOTCHWAY, K.M. SCHERER, S. HOOK, C.D. STUBBS, E. WESTON, R.H. BISBY, and A.W. PARKER, "A series of flexible design adaptations to the Nikon E-C1 and E-C2 confocal microscope systems for UV, multiphoton and FLIM imaging", Journal of Microscopy, vol. 258, pp. 68-78, 2015.
  8. C.J. Slubowski, A.D. Funk, J.M. Roesner, S.M. Paulissen, and L.S. Huang, " Plasmids for C-terminal tagging in Saccharomyces cerevisiae that contain improved GFP proteins, Envy and Ivy ", Yeast, vol. 32, pp. 379-387, 2015.