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