CMCImacrocourse.tex

% Kota Miura (miura at embl.de)
% Macro Course Textbook 

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\HRule\\
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{\Large Kota Miura}\\[0.167\textheight]

{\bfseries EMBL-CMCI course II}\\[\baselineskip]
{\textcolor{Medium}{\Huge Macro Programming in ImageJ}}\\[\baselineskip]
{\small ver 2.1.1}\\
{\small \Revision}\par
\vfill

%{\Large Centre for Molecular \& Cellular Imaging\\EMBL Heidelberg\\\plogo}\par
{\Large Centre for Molecular \& Cellular Imaging\\EMBL Heidelberg}\par
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\usepackage{pdfsync}
%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}
\title{Image Processing and Analysis Course II\\
Macro Programming in ImageJ}
\author{Kota Miura\\
\\
  Centre for Molecular and Cellular Imaging,\\
  EMBL Heidelberg,\\
  Germany\\
\\
\texttt{miura@embl.de}
}

\date{\today}

%\maketitle
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\titleTH
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\begin{abstract}
\HRule
\\
\\
\textbf{Aim: Students acquire ImageJ macro programming technique 
to ease their work loads with image processing / analysis.}
\\
\\
%need to fix greek beta
Note: This textbook was written using Fiji (ImageJ 1.44e). 
When you want to distribute, please ask Kota as this textbook is progressively edited.
\\
Compiled on \today \\
$\copyright$ 2006 - 2015, Kota Miura (http://cmci.embl.de)
\\
\HRule
\end{abstract}

\begingroup
\hypersetup{linkcolor=black}
\tableofcontents
\endgroup

\clearpage
\setcounter{chapter}{2}

%\include{CMCImacrocourse_contents}
\section{Aim: Why do we write ImageJ macro?}
  \input{sections/macroAims.tex}

\section{Introduction}
  \input{sections/macroIntro.tex}

\section{Basics}
\label{sec:ImageJMacroBasics}

	\input{sections/basics/macroBasics_HelloWorld.tex}
	\input{sections/basics/macroBasics_VarStr.tex}
	\input{sections/basics/macroBasics_ParameterInput.tex}
	\input{sections/basics/macroBasics_MacroRecording.tex}
	\input{sections/basics/macroBasics_BatchProcess.tex}

\section{Conditions and Loops}
	\input{sections/macroConditionsLoops}
		\input{sections/conditionsloops/macroConditionsApplication}
		\input{sections/conditionsloops/macroWhileApplication}

\section{Advanced Topics}
\label{sec:advancedTopics}

  \input{sections/adv/macroAdv_intro}
  \input{sections/adv/macroAdv_UserFunctions}
  \input{sections/adv/macroAdv_UserFunctions_example}
  \input{sections/adv/macroAdv_MultiParameterDialog}
  \input{sections/adv/macroAdv_GlobalVariables}
  \input{sections/adv/macroAdv_StringArrays}
  \input{sections/adv/macroAdv_NumArrays}
  \input{sections/adv/macroAdv_ArrayFunctions}
  \input{sections/adv/macroAdv_ArrayApplications}
  \input{sections/adv/macroAdv_ArrayApplications_SegmentedROI}

\section{File I/O}

	\input{sections/io/macroIO_intro}
	\input{sections/io/macroIO_resultsSaving}
	\input{sections/io/macroIO_batchProcess}
	\input{sections/io/macroIO_WorkingWithStrings}

\section{Secondary Measurement}
	\input{sections/secondaryMeasurements}

\section{Using Javascript}
	\input{sections/javascript}

\section{Actual Macro programming}
	\input{sections/ActualProgramming}

\section{Homework}
	\input{sections/homeworks}

\section{Appendix}
	\input{sections/adv/appendix_arrayReturnFunctions}

\end{document}