Paper Roundup – June 2015

  • Quantification of cell cycle state for tumor xenografts using in vivo imaging and computational image analysis [1]
  • Automated imaging and analysis of the yeast proteome [2]
  • A review of fluorogenic protein labeling [3]
  • Fluorescent proteins containing multiple copies of an epitope tag as bright immunofluorescence targets [4]
  • Using uptake of multiple dyes to map neuronal projections [5]
  • A review of correlative light and electron microscopy [6]
  • A review of novel fluorescent protein technologies [7]
  • A swept-focus light sheet microscope, using a cylindrical lens to generate a light sheet whose focus is swept through the sample [8]
  • A nice review of different commercial SIM implementations [9]
  • An open-top SPIM system for imaging samples in plates or in microfluidic devices [10]
  • A review of LOV-based reporters for fluorescence imaging [11]
  • A protocol for fixing yeast for single molecule localization microscopy [12]
  • A review of near-infrared fluorescent proteins [13]


  1. D.R. Chittajallu, S. Florian, R.H. Kohler, Y. Iwamoto, J.D. Orth, R. Weissleder, G. Danuser, and T.J. Mitchison, "In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy", Nature Methods, vol. 12, pp. 577-585, 2015.
  2. Y. Chong, J. Koh, H. Friesen, S. Kaluarachchi Duffy, M. Cox, A. Moses, J. Moffat, C. Boone, and B. Andrews, "Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis", Cell, vol. 161, pp. 1413-1424, 2015.
  3. M.P. Bruchez, "Dark dyes–bright complexes: fluorogenic protein labeling", Current Opinion in Chemical Biology, vol. 27, pp. 18-23, 2015.
  4. S. Viswanathan, M.E. Williams, E.B. Bloss, T.J. Stasevich, C.M. Speer, A. Nern, B.D. Pfeiffer, B.M. Hooks, W. Li, B.P. English, T. Tian, G.L. Henry, J.J. Macklin, R. Patel, C.R. Gerfen, X. Zhuang, Y. Wang, G.M. Rubin, and L.L. Looger, "High-performance probes for light and electron microscopy", Nature Methods, vol. 12, pp. 568-576, 2015.
  5. S. Tsuriel, S. Gudes, R.W. Draft, A.M. Binshtok, and J.W. Lichtman, "Multispectral labeling technique to map many neighboring axonal projections in the same tissue", Nature Methods, vol. 12, pp. 547-552, 2015.
  6. P. de Boer, J.P. Hoogenboom, and B.N.G. Giepmans, "Correlated light and electron microscopy: ultrastructure lights up!", Nature Methods, vol. 12, pp. 503-513, 2015.
  7. J.R. Enterina, L. Wu, and R.E. Campbell, "Emerging fluorescent protein technologies", Current Opinion in Chemical Biology, vol. 27, pp. 10-17, 2015.
  8. K. Dean, P. Roudot, E. Welf, G. Danuser, and R. Fiolka, "Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy", Biophysical Journal, vol. 108, pp. 2807-2815, 2015.
  9. K. Marno, L. Al’Zoubi, M. Pearson, M. Posch, . McKnight, and A.P. Wheeler, "The evolution of structured illumination microscopy in studies of HIV", Methods, vol. 88, pp. 20-27, 2015.
  10. R. McGorty, H. Liu, D. Kamiyama, Z. Dong, S. Guo, and B. Huang, "Open-top selective plane illumination microscope for conventionally mounted specimens", Optics Express, vol. 23, pp. 16142, 2015.
  11. A.M. Buckley, J. Petersen, A.J. Roe, G.R. Douce, and J.M. Christie, "LOV-based reporters for fluorescence imaging", Current Opinion in Chemical Biology, vol. 27, pp. 39-45, 2015.
  12. C. Kaplan, and H. Ewers, "Optimized sample preparation for single-molecule localization-based superresolution microscopy in yeast", Nature Protocols, vol. 10, pp. 1007-1021, 2015.
  13. D.M. Shcherbakova, M. Baloban, and V.V. Verkhusha, "Near-infrared fluorescent proteins engineered from bacterial phytochromes", Current Opinion in Chemical Biology, vol. 27, pp. 52-63, 2015.

New Sony Back-illuminated CMOS camera

Sony announced a new camera today that features a 42 megapixel back-illuminated CMOS sensor. I’m not that interested in the camera, but the sensor sounds pretty intriguing. No back illuminated CMOS sensors have yet made it to the scientific imaging world that I’m aware of, but we’ve all been eagerly awaiting them. It’s not clear how well a monochrome version of this Sony sensor would perform for microscopy, but the prospect of a back-illuminated CMOS sensor is pretty tantalizing. The other sensor that Sony announced, a back-illuminated, stacked sensor, also looks pretty interesting, although I understand the details less well. As far as I can tell there are no data sheets for the sensors themselves.

While trying to learn more about these sensors, I also came across this interesting page from Chipworks, comparing sensors in different Nikon cameras and their specifications.

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.