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    r169 r170  
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    11254 }
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    11307 }
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    11399   booktitle = {International Conference on Information Sciences and Systems}
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    11401 @article{Barnard1980,
    11402   author = {Barnard, S.T. and Thompson, W.B.},
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    11421   title = {Variance-Reducing Modifications for Estimators of Dependence in Random Sets},
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    11424   address = {Chicago, USA},
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    11437   address = {Berlin},
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    11439 }
    11440 @inproceedings{Dijk2002,
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    11447   publisher = {ASCI},
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    11450 }
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    11453   title = {Localization and segmentation of aortic endografts using marker detection},
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    11469 }
    11470 @phdthesis{Robbins1996,
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    11516   title = {Algorithms for 2D and 3D Image Description Based on the IAS},
    11517   year = {1990},
    11518   institution = {University of North Carolina, U.S.A.},
    11519   note = {TR90-034}
    11520 }
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    11523   title = {Maximum Likelihood from Incomplete Data via the {EM} algorithm},
    11524   journal = {Journal of the Royal Statistical Society B},
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    11528 }
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    11544   month = {June 9-11},
    11545   booktitle = {Proceedings of the 10th Scandinavian Conference on Image Analysis (Lappeenranta, Finland)}
    11546 }
    11547 @article{Perona1998,
    11548   author = {Perona, P.},
    11549   title = {Orientation Diffusions},
    11550   journal = {IEEE Transactions on Image Processing},
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    11557 @phdthesis{Borga1998,
    11558   author = {Borga, M.},
    11559   title = {Learning Multidimensional Signal Processing},
    11560   year = {1998},
    11561   address = {{Link\"oping, Sweden}},
    11562   school = {{Link\"oping University}}
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    11566   title = {Scale-Space and Edge Detection Using Anisotropic Diffusion},
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    11580   booktitle = {MICCAI'01}
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    11584   title = {Deformable Models for Early Vision},
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    11601   title = {Visualizing {RNA} molecules inside the nucleus of living cells},
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    11609   author = {Dirks, R.W. and Molenaar, R.W. and Tanke, H.J.},
    11610   title = {Methods for visualizing RNA processing and transport pathways in living cells},
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    11634   author = {Bangham, J.A. and Chardaire, P. and Pye, C.J. and Ling, P.D.},
    11635   title = {Multiscale Nonlinear Decomposition: The Sieve Decomposition Theorem},
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    11674   journal = {Neural Networks},
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    11690   title = {Beyond {Rayleighs} criterion: {A} resolution measure with application to single-molecule microscopy},
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    11699   title = {Measurement of specimen induced aberrations of biological samples using phase stepping interferometry},
    11700   journal = {Journal of Microscopy},
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    11707   author = {Schwertner, M. and Booth, M.J. and Wilson, T.},
    11708   title = {Simulation of specimen-induced aberrations for objects with spherical and cylindrical symmetry},
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    11716   author = {Simoncelli, E.P. and Freeman, W.T. and Adelson, E.H. and Heeger, D.J.},
    11717   title = {Shiftable Multi-scale Transforms},
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    11726   author = {Simoncelli, E.P. and Farid, H.},
    11727   title = {Steerable wedge filters for local orientation analysis},
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    11735   author = {Viero, T. and Jeulin, D.},
    11736   title = {Morphological Extraction of Line Networks from Noisy Low-Contrast Images},
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    11744 @article{Simoncelli1990,
    11745   author = {Simoncelli, E.P. and Adelson, E.H.},
    11746   title = {Non-Separable Extensions of Quadrature Mirror Filters to Multiple Dimensions},
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     11225 
  • qipapers.html

    r169 r170  
    1414     (see http://www.lri.fr/~filliatr/bibtex2html/),
    1515     with the following command:
    16      /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmpWQXdqi.bib  -->
     16     /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmp0UQe6y.bib  -->
    1717
    1818<h1>qipapers.html</h1>
     
    2967929679<td class="bibtexitem">
    2968029680A.&nbsp;Egner, C.&nbsp;Geisler, C.&nbsp;Von&nbsp;Middendorff, H.&nbsp;Bock, D.&nbsp;Wenzel, R.&nbsp;Medda,
    29681   M.&nbsp;Andresen, A.&nbsp;C. Stiel, S.&nbsp;Jakobs, C.&nbsp;Eggeling, A.&nbsp;Schonle, and S.&nbsp;W. Hell.
     29681  M.&nbsp;Andresen, A.&nbsp;C. Stiel, S.&nbsp;Jakobs, C.&nbsp;Eggeling, A.&nbsp;Sch&ouml;nle, and S.&nbsp;W.
     29682  Hell.
    2968229683 Fluorescence nanoscopy in whole cells by asynchronous localization of
    2968329684  photoswitching emitters.
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