Paper roundup – May 2014

  • A new SIM reconstruction algorithm that minimizes negative pixel values [1]
  • A microfluidic chemostat that traps cells in the fluid phase without contact with the device walls [2]
  • The forthcoming issue of Current Opinion in Chemical Biology is focused on imaging, including reviews on high speed biological imaging [3], quantitative super-resolution microscopy [4], and live cell reporters [5], as well as many others.
  • A description of a software system for automated mosaicing and and segmentation of large (250 GB) data sets, using the Farsight Toolkit [6]
  • Neuron labeling with fluorescent nanodiamonds [7]
  • A protocol for generating DNA origami structures for super-resolution calibration [8]
  • Building a simple light sheet microscope for imaging C. elegans [9]
  • A review of live imaging in Drosophila [10]
  • An improved infrared fluorescent protein, iFP2.0, and coexpression of heme oxygenase, give improved near-infrared imaging in neurons and in animals [11]
  • A simulator for partially coherent imaging [12]
  • Simultaneous 3D imaging of neuronal activity using light-field microscopy [13]
  • An exhortation for biologists doing fluorescence imaging to quantify the number of molecules they observe [14]
  • A review of methods for optical control of protein function [15]
  • A smartphone-based microscope using lensless imaging, with multiple illumination angles acquired by tilting the device by hand [16]
  • A new peptide-lipid conjugate, mCLING, that can be used for labeling cell membranes. It is fixable, and can be functionalized with many different dyes. [17]
  • A protein-complementation assay using an infrared fluorescent protein [18]
  • A simple flat-fielding approach for well by well correction in high throughput imaging [19]
  • Reflective confocal imaging of myelinated axons [20]
  • New photoactivatible proteins for super-resolution imaging with minimal aggregation [21]

References

  1. C.H. Righolt, S. Mai, L.J. van Vliet, and S. Stallinga, "Three-dimensional structured illumination microscopy using Lukosz bound apodization reduces pixel negativity at no resolution cost", Optics Express, vol. 22, pp. 11215, 2014. http://dx.doi.org/10.1364/OE.22.011215
  2. E.M. Johnson-Chavarria, U. Agrawal, M. Tanyeri, T.E. Kuhlman, and C.M. Schroeder, "Automated single cell microbioreactor for monitoring intracellular dynamics and cell growth in free solution", Lab Chip, vol. 14, pp. 2688-2697, 2014. http://dx.doi.org/10.1039/C4LC00057A
  3. P.W. Winter, and H. Shroff, "Faster fluorescence microscopy: advances in high speed biological imaging", Current Opinion in Chemical Biology, vol. 20, pp. 46-53, 2014. http://dx.doi.org/10.1016/j.cbpa.2014.04.008
  4. N. Durisic, L.L. Cuervo, and M. Lakadamyali, "Quantitative super-resolution microscopy: pitfalls and strategies for image analysis", Current Opinion in Chemical Biology, vol. 20, pp. 22-28, 2014. http://dx.doi.org/10.1016/j.cbpa.2014.04.005
  5. I.R. Corrêa, "Live-cell reporters for fluorescence imaging", Current Opinion in Chemical Biology, vol. 20, pp. 36-45, 2014. http://dx.doi.org/10.1016/j.cbpa.2014.04.007
  6. N. Rey-Villamizar, V. Somasundar, M. Megjhani, Y. Xu, Y. Lu, R. Padmanabhan, K. Trett, W. Shain, and B. Roysam, "Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python", Frontiers in Neuroinformatics, vol. 8, 2014. http://dx.doi.org/10.3389/fninf.2014.00039
  7. T. Hsu, K. Liu, H. Chang, E. Hwang, and J. Chao, "Labeling of neuronal differentiation and neuron cells with biocompatible fluorescent nanodiamonds", Scientific Reports, vol. 4, 2014. http://dx.doi.org/10.1038/srep05004
  8. J.J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, "DNA origami–based standards for quantitative fluorescence microscopy", Nature Protocols, vol. 9, pp. 1367-1391, 2014. http://dx.doi.org/10.1038/nprot.2014.079
  9. C. Chardès, P. Mélénec, V. Bertrand, and P. Lenne, "Setting Up a Simple Light Sheet Microscope for In Toto Imaging of C. elegans Development", Journal of Visualized Experiments, 2014. http://dx.doi.org/10.3791/51342
  10. E. Rebollo, K. Karkali, F. Mangione, and E. Martín-Blanco, "Live imaging in Drosophila: The optical and genetic toolkits", Methods, vol. 68, pp. 48-59, 2014. http://dx.doi.org/10.1016/j.ymeth.2014.04.021
  11. D. Yu, W.C. Gustafson, C. Han, C. Lafaye, M. Noirclerc-Savoye, W. Ge, D.A. Thayer, H. Huang, T.B. Kornberg, A. Royant, L.Y. Jan, Y.N. Jan, W.A. Weiss, and X. Shu, "An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging", Nature Communications, vol. 5, 2014. http://dx.doi.org/10.1038/ncomms4626
  12. S.B. Mehta, and R. Oldenbourg, "Image simulation for biological microscopy: microlith", Biomedical Optics Express, vol. 5, pp. 1822, 2014. http://dx.doi.org/10.1364/BOE.5.001822
  13. 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. http://dx.doi.org/10.1038/nmeth.2964
  14. V.C. Coffman, and J. Wu, "Every laboratory with a fluorescence microscope should consider counting molecules", Molecular Biology of the Cell, vol. 25, pp. 1545-1548, 2014. http://dx.doi.org/10.1091/mbc.E13-05-0249
  15. A.S. Baker, and A. Deiters, "Optical Control of Protein Function through Unnatural Amino Acid Mutagenesis and Other Optogenetic Approaches", ACS Chemical Biology, vol. 9, pp. 1398-1407, 2014. http://dx.doi.org/10.1021/cb500176x
  16. S.A. Lee, and C. Yang, "A smartphone-based chip-scale microscope using ambient illumination", Lab Chip, vol. 14, pp. 3056-3063, 2014. http://dx.doi.org/10.1039/C4LC00523F
  17. N.H. Revelo, D. Kamin, S. Truckenbrodt, A.B. Wong, K. Reuter-Jessen, E. Reisinger, T. Moser, and S.O. Rizzoli, "A new probe for super-resolution imaging of membranes elucidates trafficking pathways", The Journal of Cell Biology, vol. 205, pp. 591-606, 2014. http://dx.doi.org/10.1083/jcb.201402066
  18. E. Tchekanda, D. Sivanesan, and S.W. Michnick, "An infrared reporter to detect spatiotemporal dynamics of protein-protein interactions", Nature Methods, vol. 11, pp. 641-644, 2014. http://dx.doi.org/10.1038/nmeth.2934
  19. A.D. Coster, C. Wichaidit, S. Rajaram, S.J. Altschuler, and L.F. Wu, "A simple image correction method for high-throughput microscopy", Nature Methods, vol. 11, pp. 602-602, 2014. http://dx.doi.org/10.1038/nmeth.2971
  20. A.J. Schain, R.A. Hill, and J. Grutzendler, "Label-free in vivo imaging of myelinated axons in health and disease with spectral confocal reflectance microscopy", Nature Medicine, vol. 20, pp. 443-449, 2014. http://dx.doi.org/10.1038/nm.3495
  21. S. Wang, J.R. Moffitt, G.T. Dempsey, X.S. Xie, and X. Zhuang, "Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging", Proceedings of the National Academy of Sciences, vol. 111, pp. 8452-8457, 2014. http://dx.doi.org/10.1073/pnas.1406593111

2 thoughts on “Paper roundup – May 2014

  1. Hello ,Mr Kurt. I am a graduate student from Huazhong University of Science and Technology in China.Thank you for your paper roundup sharing about the microscope.Every week, I will visit your Kurt’s Microscopy Blog to find some new articles about the microscope.I wonder how to find so many articles about the field you reserch in time.Could you tell me about it, Mr Kurt?
    Yours sincerely.

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