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Thesis.pdf committed as final
The PDF was typeset as 'draft' in the original commit. I'm committing it as final typeset version now, so I have another backup copy of the full Thesis somewhere...
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‎README.md

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# PhD-Thesis
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This is my PhD-Thesis, typeset with [LaTeX] based on the [classicthesis] theme by [Andrè Miede][miede].
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This is my PhD-Thesis, typeset with [LaTeX] based on the [classicthesis] theme by [André Miede][miede].
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The progress of writing the thesis was tracked using SVN and has been migrated to GitHub for safe-keeping after I finished my work at the [Institute of Anatomy][ana] of the [University of Bern][unibe] in Switzerland.
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‎Thesis.pdf

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‎Thesis.tex

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\documentclass[%
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draft,%
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twoside,%
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openright,%
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titlepage,%
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fleqn,%
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numbers=noenddot,%
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headinclude,
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10pt,%
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a4paper,%
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BCOR5mm,%
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footinclude,%
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cleardoublepage=empty,%
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abstract=false%
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]{scrreprt}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Packages with options that might require adjustments
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%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage[utf8]{inputenc}
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\usepackage[greek,ngerman,english]{babel}
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\usepackage[square,numbers,sort&compress]{natbib}%normal Bibliography
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\usepackage{multirow}
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\usepackage{threeparttable}
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\usepackage[fleqn]{amsmath}
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\usepackage{classicthesis-ldpkg}
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\usepackage[dvipsnames]{xcolor} % needed by tikz, so loading it before
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\usepackage{tikz}
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\usetikzlibrary{shapes,arrows,patterns}
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\usepackage{pgfplots}
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%\usetikzlibrary{pgfplotsclickable} make plots clickable
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\usepackage[version=3]{mhchem}
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\usepackage[load-configurations=abbreviations,load-configurations=binary,detect-all]{siunitx}
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\DeclareSIUnit\Molar{\textsc{m}}
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\usepackage{makeidx}
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\usepackage[shadow]{todonotes}
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\usepackage{pdfpages}
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\usepackage{isotope}
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\usepackage{xfrac}
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\usepackage[groups]{svn-multi}
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\usepackage[%
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eulerchapternumbers,%
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%drafting,
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pdfspacing,%
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subfig,%
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beramono,%
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eulermath,%
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parts]{classicthesis}
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%\usepackage[margin=1.3in]{geometry}\usepackage{setspace}\doublespacing
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%%%%%%%%%%%Watermark
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%\usepackage[firstpage]{draftwatermark} % try firstpage as option
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% \SetWatermarkLightness{0.618}
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% \SetWatermarkScale{0.618}
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% \SetWatermarkText{Special Edition}
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%%%%%%%%%%%Watermark
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\usepackage[all]{hypcap}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Re-usable information
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%%%%%%%%%%%%%%%%%%%%%%%
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\svnidlong
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{$HeadURL$}
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{$LastChangedDate$}
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{$LastChangedRevision$}
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{$LastChangedBy$}
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\svnid{$Id$}
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\svngroup{Thesis-Group}
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\newcommand{\myTitle}{High resolution tomographic imaging of the alveolar region of the mammalian lung\xspace}
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\newcommand{\myDegree}{A close look deep into the lung\xspace}
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\newcommand{\myName}{David Haberth\"ur\xspace}
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\newcommand{\myProf}{Prof.\ Dr.\ Johannes C.\ Schittny\xspace}
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\newcommand{\myOtherProf}{Dr.\ Mauricio Reyes\xspace}
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\newcommand{\mySupervisor}{Prof.\ Dr.\ Martin Frenz\xspace}
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\newcommand{\myFaculty}{Faculty of Medicine\xspace}
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\newcommand{\myDepartment}{Institute of Anatomy\xspace}
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\newcommand{\myUni}{\protect{University of Bern}\xspace}
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\newcommand{\myLocation}{Bern, Switzerland\xspace}
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\newcommand{\myTime}{May 2010\xspace}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Setup and Finetuning
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%%%%%%%%%%%%%%%%%%%%%%%
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\newcommand{\imsize}{\linewidth}
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\newlength{\abcd} % for ab..z string length calculation
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\newcommand{\myfloatalign}{\centering} % how all the floats will be aligned
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\newlength\imagewidth % needed for scalebars
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\newlength\imagescale % ditto
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\newcommand{\subfigureautorefname}{\figureautorefname} % to have subfigures named using \autoref
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%%%%%%%%%%%%%%%%%%%%%%%
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% Color (Re-Definition)
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%%%%%%%%%%%%%%%%%%%%%%%
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% according to http://is.gd/aOVVy
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\definecolor{Maroon}{RGB}{229,5,58} % redefine Maroon to unibe (Pantone 192, RGB 229,5,58)
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\definecolor{unibe-link}{RGB}{147,183,209} % define unibe-color for links (Pantone 543, RGB 147,183,209)
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\definecolor{unibe-citation}{RGB}{216,140,2} % define unibe-color for citations (Pantone 138, RGB 216,140,2)
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%%%%%%%%%%%%%%%%%%%%%%%
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% Captions look and feel
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%%%%%%%%%%%%%%%%%%%%%%%
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\captionsetup{format=hang,font=small}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Hyperreferences
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%%%%%%%%%%%%%%%%%%%%%%%
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\hypersetup{% http://www.jkrieger.de/tools/latex/hyperref.html helps!
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colorlinks=true, linktocpage=true, pdfstartpage=3, pdfstartview=FitV,%
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% uncomment the following line for black links for printing
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colorlinks=false, linktocpage=false, pdfborder={0 0 0}, pdfstartpage=3, pdfstartview=FitV,%
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breaklinks=true, pdfpagemode=UseNone, pageanchor=true, pdfpagemode=UseOutlines,%
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plainpages=false, bookmarksnumbered, bookmarksopen=true, bookmarksopenlevel=1,%
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hypertexnames=true, pdfhighlight=/O,%
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urlcolor=Maroon, linkcolor=unibe-link, citecolor=unibe-citation,%
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pdftitle={\myTitle},%
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pdfauthor={\myName, \myUni, \myFaculty},%
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pdfsubject={},%
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pdfkeywords={},%
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pdfcreator={pdfLaTeX},%
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pdfproducer={LaTeX with hyperref and classicthesis}%
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}
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%%%%%%%%%%%%%%%%%%%%%%%
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% GO!GO!GO! MOVE IT!
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%%%%%%%%%%%%%%%%%%%%%%%
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\begin{document}
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\raggedbottom
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\selectlanguage{english} % english and ngerman are set up by babel
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\pagenumbering{roman}
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\pagestyle{plain}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Frontmatter
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%%%%%%%%%%%%%%%%%%%%%%%
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\include{FrontBackmatter/DirtyTitlepage}
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\cleardoublepage\include{FrontBackmatter/Titlepage}
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\include{FrontBackmatter/Titleback}
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\cleardoublepage\include{FrontBackmatter/Acceptance}
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\cleardoublepage\include{FrontBackmatter/Dedication}
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\cleardoublepage\include{FrontBackmatter/AbstractE}
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\cleardoublepage\include{FrontBackmatter/AbstractD}
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\cleardoublepage\include{FrontBackmatter/Acknowledgments}
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\pagestyle{scrheadings}
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\cleardoublepage\include{FrontBackmatter/Contents}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Mainmatter
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%%%%%%%%%%%%%%%%%%%%%%%
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\pagenumbering{arabic}
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\cleardoublepage\myPart{Introduction}\label{part:introduction}
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\include{Chapters/Introduction}
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\include{Chapters/TheMammalianLung}
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\include{Chapters/CTandTomcat}
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%%%%%%%%%%%%%%%%%%%%%%%
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\cleardoublepage\myPart{Results}\label{part:results}
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\include{Chapters/Publications}
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\include{Chapters/XRM2008}
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\include{Chapters/Tsuda2008}
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\include{Chapters/Haberthuer2010}
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%%%%%%%%%%%%%%%%%%%%%%
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\cleardoublepage\myPart{Discussion \& Outlook}\label{part:discussion}
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\include{Chapters/Discussion}
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\include{Chapters/Outlook}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Backmatter
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%%%%%%%%%%%%%%%%%%%%%%%
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\cleardoublepage\myPart{Back Matter}\label{part:back matter}
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\cleardoublepage\include{FrontBackmatter/CurriculumVitae}
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\cleardoublepage\include{FrontBackmatter/Bibliography}
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\cleardoublepage\include{FrontBackmatter/Declaration}
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\cleardoublepage\include{FrontBackmatter/Colophon}
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%%\cleardoublepage\include{FrontBackmatter/SpecialNinaAcknowledgments}
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\documentclass[%
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%draft,%
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twoside,%
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openright,%
5+
titlepage,%
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fleqn,%
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numbers=noenddot,%
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headinclude,
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10pt,%
10+
a4paper,%
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BCOR5mm,%
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footinclude,%
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cleardoublepage=empty,%
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abstract=false%
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]{scrreprt}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Packages with options that might require adjustments
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%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage[utf8]{inputenc}
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\usepackage[greek,ngerman,english]{babel}
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\usepackage[square,numbers,sort&compress]{natbib}%normal Bibliography
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\usepackage{multirow}
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\usepackage{threeparttable}
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\usepackage[fleqn]{amsmath}
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\usepackage{classicthesis-ldpkg}
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\usepackage[dvipsnames]{xcolor} % needed by tikz, so loading it before
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\usepackage{tikz}
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\usetikzlibrary{shapes,arrows,patterns}
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\usepackage{pgfplots}
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%\usetikzlibrary{pgfplotsclickable} make plots clickable
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\usepackage[version=3]{mhchem}
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\usepackage[load-configurations=abbreviations,load-configurations=binary,detect-all]{siunitx}
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\DeclareSIUnit\Molar{\textsc{m}}
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\usepackage{makeidx}
35+
\usepackage[shadow]{todonotes}
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\usepackage{pdfpages}
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\usepackage{isotope}
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\usepackage{xfrac}
39+
\usepackage[groups]{svn-multi}
40+
\usepackage[%
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eulerchapternumbers,%
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%drafting,
43+
pdfspacing,%
44+
subfig,%
45+
beramono,%
46+
eulermath,%
47+
parts]{classicthesis}
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%\usepackage[margin=1.3in]{geometry}\usepackage{setspace}\doublespacing
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%%%%%%%%%%%Watermark
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%\usepackage[firstpage]{draftwatermark} % try firstpage as option
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% \SetWatermarkLightness{0.618}
52+
% \SetWatermarkScale{0.618}
53+
% \SetWatermarkText{Special Edition}
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%%%%%%%%%%%Watermark
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\usepackage[all]{hypcap}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Re-usable information
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%%%%%%%%%%%%%%%%%%%%%%%
59+
\svnidlong
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{$HeadURL$}
61+
{$LastChangedDate$}
62+
{$LastChangedRevision$}
63+
{$LastChangedBy$}
64+
\svnid{$Id$}
65+
\svngroup{Thesis-Group}
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\newcommand{\myTitle}{High resolution tomographic imaging of the alveolar region of the mammalian lung\xspace}
67+
\newcommand{\myDegree}{A close look deep into the lung\xspace}
68+
\newcommand{\myName}{David Haberth\"ur\xspace}
69+
\newcommand{\myProf}{Prof.\ Dr.\ Johannes C.\ Schittny\xspace}
70+
\newcommand{\myOtherProf}{Dr.\ Mauricio Reyes\xspace}
71+
\newcommand{\mySupervisor}{Prof.\ Dr.\ Martin Frenz\xspace}
72+
\newcommand{\myFaculty}{Faculty of Medicine\xspace}
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\newcommand{\myDepartment}{Institute of Anatomy\xspace}
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\newcommand{\myUni}{\protect{University of Bern}\xspace}
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\newcommand{\myLocation}{Bern, Switzerland\xspace}
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\newcommand{\myTime}{May 2010\xspace}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Setup and Finetuning
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%%%%%%%%%%%%%%%%%%%%%%%
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\newcommand{\imsize}{\linewidth}
81+
\newlength{\abcd} % for ab..z string length calculation
82+
\newcommand{\myfloatalign}{\centering} % how all the floats will be aligned
83+
\newlength\imagewidth % needed for scalebars
84+
\newlength\imagescale % ditto
85+
\newcommand{\subfigureautorefname}{\figureautorefname} % to have subfigures named using \autoref
86+
%%%%%%%%%%%%%%%%%%%%%%%
87+
% Color (Re-Definition)
88+
%%%%%%%%%%%%%%%%%%%%%%%
89+
% according to http://is.gd/aOVVy
90+
\definecolor{Maroon}{RGB}{229,5,58} % redefine Maroon to unibe (Pantone 192, RGB 229,5,58)
91+
\definecolor{unibe-link}{RGB}{147,183,209} % define unibe-color for links (Pantone 543, RGB 147,183,209)
92+
\definecolor{unibe-citation}{RGB}{216,140,2} % define unibe-color for citations (Pantone 138, RGB 216,140,2)
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%%%%%%%%%%%%%%%%%%%%%%%
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% Captions look and feel
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%%%%%%%%%%%%%%%%%%%%%%%
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\captionsetup{format=hang,font=small}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Hyperreferences
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%%%%%%%%%%%%%%%%%%%%%%%
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\hypersetup{% http://www.jkrieger.de/tools/latex/hyperref.html helps!
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colorlinks=true, linktocpage=true, pdfstartpage=3, pdfstartview=FitV,%
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% uncomment the following line for black links for printing
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colorlinks=false, linktocpage=false, pdfborder={0 0 0}, pdfstartpage=3, pdfstartview=FitV,%
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breaklinks=true, pdfpagemode=UseNone, pageanchor=true, pdfpagemode=UseOutlines,%
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plainpages=false, bookmarksnumbered, bookmarksopen=true, bookmarksopenlevel=1,%
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hypertexnames=true, pdfhighlight=/O,%
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urlcolor=Maroon, linkcolor=unibe-link, citecolor=unibe-citation,%
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pdftitle={\myTitle},%
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pdfauthor={\myName, \myUni, \myFaculty},%
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pdfsubject={},%
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pdfkeywords={},%
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pdfcreator={pdfLaTeX},%
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pdfproducer={LaTeX with hyperref and classicthesis}%
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}
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%%%%%%%%%%%%%%%%%%%%%%%
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% GO!GO!GO! MOVE IT!
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%%%%%%%%%%%%%%%%%%%%%%%
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\begin{document}
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\raggedbottom
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\selectlanguage{english} % english and ngerman are set up by babel
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\pagenumbering{roman}
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\pagestyle{plain}
123+
%%%%%%%%%%%%%%%%%%%%%%%
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% Frontmatter
125+
%%%%%%%%%%%%%%%%%%%%%%%
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\include{FrontBackmatter/DirtyTitlepage}
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\cleardoublepage\include{FrontBackmatter/Titlepage}
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\include{FrontBackmatter/Titleback}
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\cleardoublepage\include{FrontBackmatter/Acceptance}
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\cleardoublepage\include{FrontBackmatter/Dedication}
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\cleardoublepage\include{FrontBackmatter/AbstractE}
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\cleardoublepage\include{FrontBackmatter/AbstractD}
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\cleardoublepage\include{FrontBackmatter/Acknowledgments}
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\pagestyle{scrheadings}
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\cleardoublepage\include{FrontBackmatter/Contents}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Mainmatter
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%%%%%%%%%%%%%%%%%%%%%%%
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\pagenumbering{arabic}
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\cleardoublepage\myPart{Introduction}\label{part:introduction}
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\include{Chapters/Introduction}
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\include{Chapters/TheMammalianLung}
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\include{Chapters/CTandTomcat}
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%%%%%%%%%%%%%%%%%%%%%%%
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\cleardoublepage\myPart{Results}\label{part:results}
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\include{Chapters/Publications}
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\include{Chapters/XRM2008}
148+
\include{Chapters/Tsuda2008}
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\include{Chapters/Haberthuer2010}
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%%%%%%%%%%%%%%%%%%%%%%
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\cleardoublepage\myPart{Discussion \& Outlook}\label{part:discussion}
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\include{Chapters/Discussion}
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\include{Chapters/Outlook}
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%%%%%%%%%%%%%%%%%%%%%%%
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% Backmatter
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%%%%%%%%%%%%%%%%%%%%%%%
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\cleardoublepage\myPart{Back Matter}\label{part:back matter}
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\cleardoublepage\include{FrontBackmatter/CurriculumVitae}
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\cleardoublepage\include{FrontBackmatter/Bibliography}
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\cleardoublepage\include{FrontBackmatter/Declaration}
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\cleardoublepage\include{FrontBackmatter/Colophon}
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%%\cleardoublepage\include{FrontBackmatter/SpecialNinaAcknowledgments}
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\end{document}

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