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    r150 r151  
    1340713407  pages = {1-9}
    1340813408}
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    13439 }
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    13462 }
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    13464   author = {Erni, R. and Freitag, B. and Hartel, P. and {M\"uller}, H. and Tiemeijer, P. and Stam, M. van der and Stekelenburg, M. and Hubert, D. and Specht, P. and Garibay-Febles, V.},
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    13470 }
    13471 @article{Erni2007,
    13472   author = {Erni, R. and Browning, N.D.},
    13473   title = {Quantification of the size-dependent energy gap of individual {CdSe} quantum dots by valence electron energy-loss spectroscopy},
    13474   journal = {Ultramicroscopy},
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    13478 }
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    13480   author = {Peng, Y. and Nellist, P.D. and Pennycook, S.J.},
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    13488   author = {Erni, R. and Lazar, S. and Browning, N.D.},
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    13490   journal = {Ultramicroscopy},
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    13494 }
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    13496   author = {Erni, R. and Rossell, M.D. and Kisielowski, C. and Dahmen, U.},
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    13566   note = {sold out, reprint 2006}
    13567 }
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    13569   author = {{B\"ottcher}, B.},
    13570   title = {Electron cryo-micrsocopy of graphite in amorphous ice},
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    13575 }
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    13578   title = {Phase retrieval through focus variation for ultra-resolution in field-emission transmission electron microscopy},
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    13585 @article{Atsuzawa2009,
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    13595   title = {Performance Evaluation of a Transmission Scintillator-Based Lens-Coupled 4K CCD Camera for Use in Low-Dose Electron Cryo-Microscopy},
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    13633 }
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    13691 }
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    13709 @article{Nellist1998,
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    13711   title = {Subangstrom Resolution by Underfocused Incoherent Transmission Electron Microscopy},
    13712   journal = {Physical Review Letters},
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    13717 }
    13718 @article{Yonekura2006,
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    13721   journal = {Journal of Structural Biology},
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    13729   journal = {Ultramicroscopy},
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    13736   title = {Range of validity of field emission equations},
    13737   journal = {Journal of Vaccuum Science Technology B},
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    13739   volume = {26},
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    13761   title = {Projection structure of Halorhodopsin from Halobacterium halobium at 6 {\AA} resolution obtrained by electron cryo-microscopy},
    13762   journal = {Journal of Molecular Biology},
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    13769   title = {Three-dimensional structure of halorhodopsin at 7 {\AA} resolution},
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    13775 @article{Ruprecht2001,
    13776   author = {Ruprecht, J. and Nield, J.},
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    13783 @article{Pennycook2000,
    13784   author = {Pennycook, S.J. and Rafferty, B. and Nellist, P.D.},
    13785   title = {Z-Contrast Imaging in an Aberration-Corrected Scanning Transmission Electron Microscope},
    13786   journal = {Microscopy and Microanalysis},
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    13788   volume = {6},
    13789   pages = {343}
    13790 }
    13791 @inproceedings{Pennycook2003,
    13792   author = {Pennycook, S.J. and Lupini, A.R. and Varela, M. and Borisevich, A. and Peng, Y. and Nellist, P.D.},
    13793   title = {Quantum Mechanical Resolution Limits to Imaging and Spectroscopy in the Transmission Electron Microscope},
    13794   year = {2003},
    13795   pages = {126},
    13796   editor = {McGuire, J.},
    13797   publisher = {Old Dominion Universtity},
    13798   booktitle = {From the Atomic to the Nano Scale}
    13799 }
    13800 @article{Pennycook2009,
    13801   author = {Zach2009},
    13802   title = {Aberration corrected scanning transmission electron microscopy: from atomic imaging and analysis to solving energy problems},
    13803   journal = {Philosophical Transactions of the Royal Society},
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    13808 @article{Pennycook1990,
    13809   author = {Pennycook, S.J. and Jesson, D.E.},
    13810   title = {High-Resolution Incoherent Imaging of Crystals},
    13811   journal = {Physical Review Letters},
    13812   year = {1990},
    13813   volume = {64},
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    13816 @article{Muto2006a,
    13817   author = {Muto, S. and Tatsumi, K. and Puetter, R.C. and Yosida, T. and Yamamoto, Y. and Sasano, Y.},
    13818   title = {Spectral restoration and energy resolution improvement of electron energy-loss spectra by Pixon reconstruction: {II. Application} to practical {ELNES} analysis of low {SNR}},
    13819   journal = {Journal of Electron Microscopy},
    13820   year = {2006},
    13821   volume = {55},
    13822   number = {4},
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    13824 }
    13825 @article{Kujawa1990,
    13826   author = {Kujawa, S. and Krahl, D. and Niedrig, H. and Zeitler, E.},
    13827   title = {Second-rank aberrations of a magnetic imaging energy filter: measurement and correction},
    13828   journal = {Optik},
    13829   year = {1990},
    13830   volume = {86},
    13831   pages = {39-46}
    13832 }
    13833 @article{Kujawa1992,
    13834   author = {Kujawa, S. and Krahl, D.},
    13835   title = {Performance of a low-noise CCD camera adapted to a transmission electron microscope},
    13836   journal = {Ultramicrosopy},
    13837   year = {1992},
    13838   volume = {46},
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    13840 }
    13841 @article{Lugg2010,
    13842   author = {Lugg, N.R. and Freitag, B. and Findlay, S.D. and Allen, L.J..},
    13843   title = {Energy-filtered transmission electron microscopy based on inner-shell ionization},
    13844   journal = {Ultramicroscopy},
    13845   year = {2010}
    13846 }
    13847 @article{Avoort2005,
    13848   author = {Avoort, C. van der and Braat, J.J.M. and Dirksen, P. and Janssen, A.J.E.M.},
    13849   title = {Aberration retrieval from the intensity point-spread function in the focal region using the extended {Nijboer-Zernike} approach},
    13850   journal = {Journal of Modern Optics},
    13851   year = {2005},
    13852   volume = {52},
    13853   number = {12},
    13854   pages = {1695-1728}
    13855 }
    13856 @article{Eastham2009,
    13857   author = {Eastham, D.A. and Edmondson, P. and Greene, S. and Donnelly, S. and Olsson, E. and Svensson, K. and Bleloch, A.},
    13858   title = {A design for a subminiature, low energy scanning electron microscope with atomic resolution},
    13859   journal = {Journal of Appplied Physics},
    13860   year = {2009},
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    13864 @article{Schonhense2002,
    13865   author = {{Sch\"onhense}, G. and Spiecker, H.},
    13866   title = {Correction of chromatic and spherical aberration in electron microscopy utilizing the time structure of pulsed excitation sources},
    13867   journal = {Journal of Vacuum Science Technology B},
    13868   year = {2002},
    13869   volume = {20},
    13870   number = {6},
    13871   pages = {2526-2534}
    13872 }
    13873 @article{Sawada2005,
    13874   author = {Sawada, H. and Tomita, T. and Naruse, M. and Honda, T. and Hambridge, P. and Hartel, P. and Haider, M. and Hetherington, C. and Doole, R. and Kirkland, A. and Hutchison, J. and Titchmarsh, J. and Cockayne, D.},
    13875   title = {Experimental evaluation of a spherical aberration-corrected {TEM} and {STEM}},
    13876   journal = {Journal of Electron Microscopy},
    13877   year = {2005},
    13878   volume = {54},
    13879   number = {2},
    13880   pages = {119-121}
    13881 }
    13882 @article{Hartel1996,
    13883   author = {Hartel, P. and Rose, H. and Dinges, C.},
    13884   title = {Conditions and reasons for incoherent imaging in {STEM}},
    13885   journal = {Ultramicroscopy},
    13886   year = {1996},
    13887   volume = {63},
    13888   pages = {93-114}
    13889 }
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     13409@arti
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    1515     with the following command:
    16      /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmp9cY3Sa.bib  -->
     16     /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmpLGg4GI.bib  -->
    1717
    1818<h1>qipapers.html</h1>
     
    3021530215</td>
    3021630216<td class="bibtexitem">
    30217 T.&nbsp;Dertinger, R&gt;&nbsp;Colyer, G.&nbsp;Iyer, S.&nbsp;Weiss, and J.&nbsp;Enderlein.
     30217T.&nbsp;Dertinger, R.&nbsp;Colyer, G.&nbsp;Iyer, S.&nbsp;Weiss, and J.&nbsp;Enderlein.
    3021830218 Fast, background-free, 3d super-resolution optical fluctuation
    3021930219  imaging (sofi).
     
    3022430224</td>
    3022530225</tr>
     30226
     30227
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     30229<td align="right" class="bibtexnumber">
     30230[<a name="Dertinger2010">2161</a>]
     30231</td>
     30232<td class="bibtexitem">
     30233T.&nbsp;Dertinger, R.&nbsp;Colyer, R.&nbsp;Vogel, J.&nbsp;Enderlein, and S.&nbsp;Weiss.
     30234 Achieving increased resolution and more pixels with superresolution
     30235  optical fluctuation imaging (sofi).
     30236 <em>Optics Express</em>, 18(18):18875-11885, 2010.
     30237
     30238</td>
     30239</tr>
    3022630240</table><hr><p><em>This file was generated by
    3022730241<a href="http://www.lri.fr/~filliatr/bibtex2html/">bibtex2html</a> 1.95.</em></p>
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