Paper Roundup – February 2014

  • A fluorescence method for measuring absolute membrane potential [1]
  • Protocols for single particle tracking using QDots, organic dyes, and gold nanoparticles [2]
  • Color calibration for microscopy, using the DataColor ChromaCal system [3]
  • A microscope that uses quantum entanglement to improve the signal to noise ratio for DIC microscopy. Not practical for biology yet, but an interesting proof-of-concept [4]
  • A nice paper describing an automated pipeline for quantifying cell number and type during growth of Arabidopsis hypocotyls [5]
  • A short article on motion compensation / drift correction in imaging applications [6]
  • A review on fixation protocols for a planarian for both histology and EM; while focused on a specific organism it is a nice discussion of how to optimize a fixation protocol [7]
  • A new genetically encoded calcium sensor based on aequorin and GFP [8]
  • An ImageJ based protocol for segmentation, colocalization, and shape analysis of subcellular objects [9]
  • A quantitative phase contrast microscopy method that allows measuring the phase shift introduced by a sample [10]. News and Views [11]
  • A review of the openSPIM and openSpinMicroscopy platforms [12]
  • A review of localization-based super-resolution with genetically encodable probes [13]
  • A review of single molecule localization precision and accuracy [14] and a review of localization algorithms [15]
  • Using transient binding of labeled DNA strands to generate super-resolution images via PAINT [16]

References

  1. J. Hou, V. Venkatachalam, and A. Cohen, "Temporal Dynamics of Microbial Rhodopsin Fluorescence Reports Absolute Membrane Voltage", Biophysical Journal, vol. 106, pp. 639-648, 2014. http://dx.doi.org/10.1016/j.bpj.2013.11.4493
  2. L. Cognet, B. Lounis, and D. Choquet, "Tracking Receptors Using Individual Fluorescent and Nonfluorescent Nanolabels", Cold Spring Harbor Protocols, vol. 2014, pp. pdb.prot080416, 2014. http://dx.doi.org/10.1101/pdb.prot080416
  3. B. Foster, and J. Sedgewick, "Color Integrity: Is What You See What You Saw?", Microscopy Today, vol. 22, pp. 12-17, 2014. http://dx.doi.org/10.1017/S1551929513001272
  4. T. Ono, R. Okamoto, and S. Takeuchi, "An entanglement-enhanced microscope", Nature Communications, vol. 4, 2013. http://dx.doi.org/10.1038/ncomms3426
  5. M. Sankar, K. Nieminen, L. Ragni, I. Xenarios, and C.S. Hardtke, "Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth", eLife, vol. 3, 2014. http://dx.doi.org/10.7554/eLife.01567
  6. B. LUCOTTE, and R. BALABAN, "Motion compensation for in vivo subcellular optical microscopy", Journal of Microscopy, vol. 254, pp. 9-12, 2014. http://dx.doi.org/10.1111/jmi.12116
  7. J.L. Brubacher, A.P. Vieira, and P.A. Newmark, "Preparation of the planarian Schmidtea mediterranea for high-resolution histology and transmission electron microscopy", Nature Protocols, vol. 9, pp. 661-673, 2014. http://dx.doi.org/10.1038/nprot.2014.041
  8. A. Rodriguez-Garcia, J. Rojo-Ruiz, P. Navas-Navarro, F.J. Aulestia, S. Gallego-Sandin, J. Garcia-Sancho, and M.T. Alonso, "GAP, an aequorin-based fluorescent indicator for imaging Ca2+ in organelles", Proceedings of the National Academy of Sciences, vol. 111, pp. 2584-2589, 2014. http://dx.doi.org/10.1073/pnas.1316539111
  9. A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I.F. Sbalzarini, "Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh", Nature Protocols, vol. 9, pp. 586-596, 2014. http://dx.doi.org/10.1038/nprot.2014.037
  10. T. Kim, R. Zhou, M. Mir, S.D. Babacan, P.S. Carney, L.L. Goddard, and G. Popescu, "White-light diffraction tomography of unlabelled live cells", Nature Photonics, vol. 8, pp. 256-263, 2014. http://dx.doi.org/10.1038/nphoton.2013.350
  11. A. Bouwens, and T. Lasser, "White-light diffraction tomography", Nature Photonics, vol. 8, pp. 173-174, 2014. http://dx.doi.org/10.1038/nphoton.2014.44
  12. E. Gualda, N. Moreno, P. Tomancak, and G.G. Martins, "Going "open" with Mesoscopy: a new dimension on multi-view imaging", Protoplasma, vol. 251, pp. 363-372, 2014. http://dx.doi.org/10.1007/s00709-013-0599-3
  13. P.N. Hedde, and G.U. Nienhaus, "Super-resolution localization microscopy with photoactivatable fluorescent marker proteins", Protoplasma, vol. 251, pp. 349-362, 2013. http://dx.doi.org/10.1007/s00709-013-0566-z
  14. H. Deschout, F.C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S.T. Hess, and K. Braeckmans, "Precisely and accurately localizing single emitters in fluorescence microscopy", Nature Methods, vol. 11, pp. 253-266, 2014. http://dx.doi.org/10.1038/nmeth.2843
  15. A. Small, and S. Stahlheber, "Fluorophore localization algorithms for super-resolution microscopy", Nature Methods, vol. 11, pp. 267-279, 2014. http://dx.doi.org/10.1038/nmeth.2844
  16. R. Jungmann, M.S. AvendaƱo, J.B. Woehrstein, M. Dai, W.M. Shih, and P. Yin, "Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT", Nature Methods, vol. 11, pp. 313-318, 2014. http://dx.doi.org/10.1038/nmeth.2835