Paper Roundup – June 2014

  • A method for recovering GFP fluorescence after resin embedding by treament with alkaline buffers [1]
  • A 3D-STORM analysis tool using compressed sensing [2]
  • A method for imaging single-copy splice variants of RNAs using plasmonic coupling of gold nanoparticles [3]
  • Improving the performance of multifocal multiphoton microscopy by reassignment of scattered photons [4]
  • A review of photoswitchable fluorescent proteins for super-resolution imaging [5]
  • 6nm resolution imaging of DNA origami using DNA-PAINT [6]
  • A temporal focusing, two-photon line microscope for rapid volumetric imaging, used to imaging neuronal activity in 3D neuronal cultures [7]
  • A review of plasmonic alternatives to FRET for determining the distance between particles at the 10 – 100 nm distance scale. [8]
  • Improved deconvolution performance using a spatially varying regularization term [9]
  • Organelle-specific calcium indicators in a variety of different colors [10]
  • A multiplexing scheme for improving the speed of Fourier Ptychographic miroscopy [11]
  • Lasing from the fluorescent protein Venus, suspended in droplets or in bacteria [12]
  • An optimized protocol for CLARITY clearing of tissues, including details of a CLARITY-optimized light sheet microscope [13]
  • A review of the uses of flatbed scanners in biomedical imaging [14]
  • Ribozymes that catalyze their own labeling with fluorescein iodoacetamide [15]
  • A comparison of probes for tracking acidic organelles [16]
  • A review of fluorescence cryo-microscopy [17]
  • The current issue of Nature Chemical Biology focuses on light, with reviews of fluorescent labeling strategies [18], photoswitchable fluorescent proteins [19], and single molecule tracking [20]
  • Measurements of Dendra2 photoconversion, blinking, and bleaching rates in cells [21]
  • A paper describing construction of a whole slide imaging microscope [22]
  • Two new fluorescent voltage sensor proteins [23], [24]
  • A light-field microscope for high speed neuronal imaging of C. elegans and zebrafish [25]
  • Correlated cryogenic PALM and cryo-electron microscope [26]


  1. H. Xiong, Z. Zhou, M. Zhu, X. Lv, A. Li, S. Li, L. Li, T. Yang, S. Wang, Z. Yang, T. Xu, Q. Luo, H. Gong, and S. Zeng, "Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging", Nature Communications, vol. 5, 2014.
  2. L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, "High-Density 3D Single Molecular Analysis Based on Compressed Sensing", Biophysical Journal, vol. 106, pp. 2443-2449, 2014.
  3. K. Lee, Y. Cui, L.P. Lee, and J. Irudayaraj, "Quantitative imaging of single mRNA splice variants in living cells", Nature Nanotechnology, vol. 9, pp. 474-480, 2014.
  4. J.W. Cha, V.R. Singh, K.H. Kim, J. Subramanian, Q. Peng, H. Yu, E. Nedivi, and P.T.C. So, "Reassignment of Scattered Emission Photons in Multifocal Multiphoton Microscopy", Scientific Reports, vol. 4, 2014.
  5. D.M. Shcherbakova, P. Sengupta, J. Lippincott-Schwartz, and V.V. Verkhusha, "Photocontrollable Fluorescent Proteins for Superresolution Imaging", Annual Review of Biophysics, vol. 43, pp. 303-329, 2014.
  6. M. Raab, J.J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, "Fluorescence Microscopy with 6 nm Resolution on DNA Origami", ChemPhysChem, vol. 15, pp. 2431-2435, 2014.
  7. H. Dana, A. Marom, S. Paluch, R. Dvorkin, I. Brosh, and S. Shoham, "Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks", Nature Communications, vol. 5, 2014.
  8. P.C. Ray, Z. Fan, R.A. Crouch, S.S. Sinha, and A. Pramanik, "Nanoscopic optical rulers beyond the FRET distance limit: fundamentals and applications", Chem. Soc. Rev., vol. 43, pp. 6370-6404, 2014.
  9. J. SEO, S. HWANG, J. LEE, and H. PARK, "Spatially varying regularization of deconvolution in 3D microscopy", Journal of Microscopy, pp. n/a-n/a, 2014.
  10. J. Suzuki, K. Kanemaru, K. Ishii, M. Ohkura, Y. Okubo, and M. Iino, "Imaging intraorganellar Ca2+ at subcellular resolution using CEPIA", Nature Communications, vol. 5, 2014.
  11. L. Tian, X. Li, K. Ramchandran, and L. Waller, "Multiplexed coded illumination for Fourier Ptychography with an LED array microscope", Biomedical Optics Express, vol. 5, pp. 2376, 2014.
  12. A. Jonáš, M. Aas, Y. Karadag, S. Manioğlu, S. Anand, D. McGloin, H. Bayraktar, and A. Kiraz, "In vitro and in vivo biolasing of fluorescent proteins suspended in liquid microdroplet cavities", Lab Chip, vol. 14, pp. 3093-3100, 2014.
  13. R. Tomer, L. Ye, B. Hsueh, and K. Deisseroth, "Advanced CLARITY for rapid and high-resolution imaging of intact tissues", Nature Protocols, vol. 9, pp. 1682-1697, 2014.
  14. Z. Göröcs, and A. Ozcan, "Biomedical imaging and sensing using flatbed scanners", Lab Chip, vol. 14, pp. 3248-3257, 2014.
  15. A.K. Sharma, J.J. Plant, A.E. Rangel, K.N. Meek, A.J. Anamisis, J. Hollien, and J.M. Heemstra, "Fluorescent RNA Labeling Using Self-Alkylating Ribozymes", ACS Chemical Biology, vol. 9, pp. 1680-1684, 2014.
  16. A. Pierzyńska-Mach, P.A. Janowski, and J.W. Dobrucki, "Evaluation of acridine orange, LysoTracker Red, and quinacrine as fluorescent probes for long-term tracking of acidic vesicles", Cytometry Part A, vol. 85, pp. 729-737, 2014.
  17. R. Kaufmann, C. Hagen, and K. Grünewald, "Fluorescence cryo-microscopy: current challenges and prospects", Current Opinion in Chemical Biology, vol. 20, pp. 86-91, 2014.
  18. K.M. Dean, and A.E. Palmer, "Advances in fluorescence labeling strategies for dynamic cellular imaging", Nature Chemical Biology, vol. 10, pp. 512-523, 2014.
  19. V. Adam, R. Berardozzi, M. Byrdin, and D. Bourgeois, "Phototransformable fluorescent proteins: Future challenges", Current Opinion in Chemical Biology, vol. 20, pp. 92-102, 2014.
  20. A. Kusumi, T.A. Tsunoyama, K.M. Hirosawa, R.S. Kasai, and T.K. Fujiwara, "Tracking single molecules at work in living cells", Nature Chemical Biology, vol. 10, pp. 524-532, 2014.
  21. S. Avilov, R. Berardozzi, M.S. Gunewardene, V. Adam, S.T. Hess, and D. Bourgeois, "In cellulo Evaluation of Phototransformation Quantum Yields in Fluorescent Proteins Used As Markers for Single-Molecule Localization Microscopy", PLoS ONE, vol. 9, pp. e98362, 2014.
  22. G. Bueno, O. Déniz, M.D.M. Fernández-Carrobles, N. Vállez, and J. Salido, "An automated system for whole microscopic image acquisition and analysis", Microscopy Research and Technique, vol. 77, pp. 697-713, 2014.
  23. Y. Gong, M.J. Wagner, J. Zhong Li, and M.J. Schnitzer, "Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors", Nature Communications, vol. 5, 2014.
  24. F. St-Pierre, J.D. Marshall, Y. Yang, Y. Gong, M.J. Schnitzer, and M.Z. Lin, "High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor", Nature Neuroscience, vol. 17, pp. 884-889, 2014.
  25. R. Prevedel, Y. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E.S. Boyden, and A. Vaziri, "Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy", Nature Methods, vol. 11, pp. 727-730, 2014.
  26. Y. Chang, S. Chen, E.I. Tocheva, A. Treuner-Lange, S. Löbach, L. Søgaard-Andersen, and G.J. Jensen, "Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography", Nature Methods, vol. 11, pp. 737-739, 2014.