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Prof. Michael Liebling
Department of Electrical on Computer Engineering
University of California Santa Barbara
Final
Each student chooses a technique paper in (broad) relation to the topics covered in class. Paper must be either in list of proposed papers or approved by instructor. Students are encouraged to choose and read their paper as early as possible. They must indicate their choice (by email) to the instructor on Tuesday January 29 at the latest, as well as short answers to (or how they intend to approach) the following questions in their final paper:
The final Text should hold on 1 letter page with 0.75in margins on all sides, set in 11 point size type (Times New Roman or similar). There is no limit on the number of references and of possible figures or tables (neither the references nor the figures or tables are included in the 1 page limit). Submission should be a PDF file whose size is not to exceed 3MB.
The final paper must be submitted (by email to the instructor) before Friday March 14, 11:59PM.
Late submission of the final will result in the following point subtractions:
| 1min to 1h late | -10 points |
| 1h 1min to 24h late | -20 points |
| 24h to 48h late | -40 points |
| 48h late and more | -80 points |
Early submissions will be accepted.
Paper Suggestions for Final
Below is a list of possible papers for you to choose from (with link to original paper, make sure you are on a campus computer to have access to the journal's homepages). You may pick one of these or choose another paper (I welcome your suggestions).
Novel Dyes and Fluorophores
D Shcherbo, E M Merzlyak, T V Chepurnykh, A F Fradkov, G V Ermakova, E A Solovieva, K A Lukyanov, E A Bogdanova, A G Zaraisky, S Lukyanov, D M ChudakovBright far-red fluorescent protein for whole-body imaging, Nature Methods - 4, 741 - 746 (2007)
Super-resolution
Gustafsson, M. G. L. (2005). Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. USA 102, 13081-13086.
Gustafsson, M. G. L., Agard, D. A., and Sedat, J. W. (1999). I5M: 3D widefield light microscopy with better than 100 nm axial resolution. J. Microsc. 195, 10-16.
Hell, S. W. (2007). Far-field optical nanoscopy. Science 316, 1153-8.
KI Willig, B Harke R Medda, S W Hell, STED microscopy with continuous wave beams, Nature Methods - 4, 915 - 918 (2007)
S Manley, J M Gillette, G H Patterson, H Shroff, H F Hess, E. Betzig, J. Lippincott-Schwartz, High-density mapping of single-molecule trajectories with photoactivated localization microscopy, Published online: 13 January 2008; | doi:10.1038/nmeth.1176
Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S.,
Davidson, M. W., Lippincott-Schwartz, J., and Hess, H. F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642-1645.
3D Microscopy
W Choi, C Fang-Yen, K Badizadegan, S Oh, N Lue, RR Dasari, M S Feld, Tomographic phase microscopy. Nature Methods - 4, 717 - 719 (2007)
Sharpe, J., Ahlgren, U., Perry, P., Hill, B., Ross, A., Hecksher-Sorensen, J., Baldock, R., and Davidson, D. (2002). Optical projection tomography as a tool for 3d microscopy and gene expression studies. Science 296, 541-5.
P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, E. H K Stelzer High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy, Nature Methods 4, 311 - 313 (2007)
Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J., and Stelzer, E. H. K. (2004). Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007-1009.
E.J. Botcherby, R. Juškaitis, M.J. Booth and T. Wilson An optical technique for remote focusing in microscopy Optics Communications, Volume 281, Issue 4, 15 February 2008, Pages 880-887
P.J. Keller, F. Pampaloni, E. H. K. Stelzer Three-dimensional preparation and imaging reveal intrinsic microtubule properties, Nature Methods 4, 843-846 (2007)
High-performance microscopy
Bewersdorf, J., Pick, R., and Hell, S. W. (1998). Multifocal multiphoton microscopy Opt. Lett. 23, 655-657.
Rueckel, M., Mack-Bucher, J. A., and Denk, W. (2006). Adaptive wavefront correction in two-photon microscopy using coherence-gated wavefront sensing. Proc. Natl. Acad. Sci. USA 103, 17137-17142.
Z. Kam, B. Hanser, M. G. L. Gustafsson , D. A. Agard, and J. W. Sedat, Computational adaptive optics for live three-dimensional biological imaging, PNAS, March 27, 2001, vol. 98, no. 7, pp. 3790-3795
Image Analysis
D. Thomann, D. R. Rines, P. K. Sorger, G. Danuser, Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement. Journal of Microscopy, Volume 208 Issue 1 Page 49-64, October 2002
W Supatto, D Débarre, B Moulia, E Brouzés, J-L Martin, E Farge, E Beaurepaire, In vivo modulation of morphogenetic movements in Drosophila embryos with femtosecond laser pulses, PNAS, January 25, 2005, vol. 102, no. 4, 1047-1052
A E Carpenter Image-based chemical screening Nature Chemical Biology 3, 461-465 (2007)
C Bakal, J Aach, G Church, N Perrimon Quantitative Morphological Signatures Define Local Signaling Networks Regulating Cell Morphology Science 22 June 2007: Vol. 316. no. 5832, pp. 1753-1756
A Gordon, A Colman-Lerner, T E Chin, KR Benjamin, R C Yu, R Brent,Single-cell quantification of molecules and rates using open-source microscope-based cytometry, Nature Methods 4, 175-181 (2007)
Neuroscience
Kazuo Kitamura, B Judkewitz M. Kano, W. Denk, Michael Häser ,Targeted patch-clamp recordings and single-cell electroporation of unlabeled neurons in vivo, Nature Methods - 5, 61 - 67 (2007)
