Paper Roundup: January 2016

  • Microscopy Image Browser: a new open source tool for image analysis and visualization, written in Matlab [1]
  • A microscopy system for imaging neuronal activity in freely moving C. elegans [2]
  • A fluorescent protein tag that features rapid reversible binding of the chromophore [3]
  • Protocols for STORM imaging in tissue sections [4]
  • Fluorescent proteins for three and four color imaging in yeast [5]
  • Selecting protein markers for optimal phenotypic screening of drugs [6]
  • A set of refined protocols for CLARITY clearing, refractive index matching, and antibody penetration called ACT-PRESTO [7]
  • Simple chemical methods for making dye-photostabilizer conjugates resulting in dyes with reduced photobleaching rates [8]
  • Proximal cyclooctatetraene is a general dye photostabilizer [9]
  • Combining Fourier ptychography, pupil function estimation, and deconvolution [10]
  • Using a spherically aberrated point spread function to improve imaging depth in light-sheet microscopy [11]
  • Fluorescent speckle microscopy by speckled photoswitching [12]
  • Whole brain two-photon imaging with clearing and integrated sectioning [13]
  • Combining STED and RESOLFT to improve contrast and photostability [14]
  • Measuring resolution in coherent microscopy (technical, but has a nice set of references for resolution limits in microscopy) [15]
  • Photoacoustic tomography with a reversibly photoswitchable probe to improve contrast [16]
  • Incorporating probes into live cells by squeezing them through a aperture [17]


  1. I. Belevich, M. Joensuu, D. Kumar, H. Vihinen, and E. Jokitalo, "Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets", PLOS Biology, vol. 14, pp. e1002340, 2016.
  2. J.P. Nguyen, F.B. Shipley, A.N. Linder, G.S. Plummer, M. Liu, S.U. Setru, J.W. Shaevitz, and A.M. Leifer, "Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans", Proceedings of the National Academy of Sciences, vol. 113, pp. E1074-E1081, 2015.
  3. M. Plamont, E. Billon-Denis, S. Maurin, C. Gauron, F.M. Pimenta, C.G. Specht, J. Shi, J. Quérard, B. Pan, J. Rossignol, K. Moncoq, N. Morellet, M. Volovitch, E. Lescop, Y. Chen, A. Triller, S. Vriz, T. Le Saux, L. Jullien, and A. Gautier, "Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo", Proceedings of the National Academy of Sciences, vol. 113, pp. 497-502, 2015.
  4. L. Barna, B. Dudok, V. Miczán, A. Horváth, Z.I. László, and I. Katona, "Correlated confocal and super-resolution imaging by VividSTORM", Nature Protocols, vol. 11, pp. 163-183, 2015.
  5. R. Higuchi-Sanabria, E.J. Garcia, D. Tomoiaga, E.L. Munteanu, P. Feinstein, and L.A. Pon, "Characterization of Fluorescent Proteins for Three- and Four-Color Live-Cell Imaging in S. cerevisiae", PLOS ONE, vol. 11, pp. e0146120, 2016.
  6. J. Kang, C. Hsu, Q. Wu, S. Liu, A.D. Coster, B.A. Posner, S.J. Altschuler, and L.F. Wu, "Improving drug discovery with high-content phenotypic screens by systematic selection of reporter cell lines", Nature Biotechnology, vol. 34, pp. 70-77, 2016.
  7. E. Lee, J. Choi, Y. Jo, J.Y. Kim, Y.J. Jang, H.M. Lee, S.Y. Kim, H. Lee, K. Cho, N. Jung, E.M. Hur, S.J. Jeong, C. Moon, Y. Choe, I.J. Rhyu, H. Kim, and W. Sun, "ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging", Scientific Reports, vol. 6, 2016.
  8. J.H.M. van der Velde, J. Oelerich, J. Huang, J.H. Smit, A. Aminian Jazi, S. Galiani, K. Kolmakov, G. Gouridis, C. Eggeling, A. Herrmann, G. Roelfes, and T. Cordes, "A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization", Nature Communications, vol. 7, 2016.
  9. Q. Zheng, S. Jockusch, G.G. Rodríguez-Calero, Z. Zhou, H. Zhao, R.B. Altman, H.D. Abruña, and S.C. Blanchard, "Intra-molecular triplet energy transfer is a general approach to improve organic fluorophore photostability", Photochemical & Photobiological Sciences, vol. 15, pp. 196-203, 2016.
  10. J. Chung, J. Kim, X. Ou, R. Horstmeyer, and C. Yang, "Wide field-of-view fluorescence image deconvolution with aberration-estimation from Fourier ptychography", Biomedical Optics Express, vol. 7, pp. 352, 2016.
  11. R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, "SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function", Cell, vol. 163, pp. 1796-1806, 2015.
  12. A.J. Pereira, P. Aguiar, M. Belsley, and H. Maiato, "Inducible fluorescent speckle microscopy", Journal of Cell Biology, vol. 212, pp. 245-255, 2016.
  13. M.N. Economo, N.G. Clack, L.D. Lavis, C.R. Gerfen, K. Svoboda, E.W. Myers, and J. Chandrashekar, "A platform for brain-wide imaging and reconstruction of individual neurons", eLife, vol. 5, 2016.
  14. J.G. Danzl, S.C. Sidenstein, C. Gregor, N.T. Urban, P. Ilgen, S. Jakobs, and S.W. Hell, "Coordinate-targeted fluorescence nanoscopy with multiple off states", Nature Photonics, vol. 10, pp. 122-128, 2016.
  15. R. Horstmeyer, R. Heintzmann, G. Popescu, L. Waller, and C. Yang, "Standardizing the resolution claims for coherent microscopy", Nature Photonics, vol. 10, pp. 68-71, 2016.
  16. J. Yao, A.A. Kaberniuk, L. Li, D.M. Shcherbakova, R. Zhang, L. Wang, G. Li, V.V. Verkhusha, and L.V. Wang, "Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe", Nature Methods, vol. 13, pp. 67-73, 2015.
  17. A. Kollmannsperger, A. Sharei, A. Raulf, M. Heilemann, R. Langer, K.F. Jensen, R. Wieneke, and R. Tampé, "Live-cell protein labelling with nanometre precision by cell squeezing", Nature Communications, vol. 7, 2016.