\begin
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%
% Complete documentation on the extended LaTeX markup used for Insight
% documentation is available in ``Documenting Insight'', which is part
% of the standard documentation for Insight. It may be found online
% at:
%
% http://www.itk.org/
\documentclass{InsightArticle}
\usepackage[utf8]{inputenc}
\usepackage{algorithm}
\usepackage{graphicx}
\usepackage{color}
\usepackage{minted}
\usepackage{xcolor}
\definecolor{ltgray}{rgb}{0.93,0.93,0.93}
\usemintedstyle{emacs}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% hyperref should be the last package to be loaded.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[bookmarks,
bookmarksopen,
backref,
colorlinks,linkcolor={blue},citecolor={blue},urlcolor={blue},
]{hyperref}
% This is a template for Papers to the Insight Journal.
% It is comparable to a technical report format.
% The title should be descriptive enough for people to be able to find
% the relevant document.
\title{The Importance of Open Access in Scientific Publications}
%
% NOTE: This is the last number of the "handle" URL that
% The Insight Journal assigns to your paper as part of the
% submission process. Please replace the number "1338" with
% the actual handle number that you get assigned.
%
\newcommand{\IJhandlerIDnumber}{1338}
% Increment the release number whenever significant changes are made.
% The author and/or editor can define 'significant' however they like.
\release{0.00}
% At minimum, give your name and an email address. You can include a
% snail-mail address if you like.
\author{Galileo Galilei$^{1}$, Giordano Bruno$^{2}$ and Anthony Leeuwenhoek$^{3}$}
\authoraddress{$^{1}$Pisa University, Tower drive\\
$^{2}$Rome University, Inquisition street\\
$^{3}$Netherlands Pragmatic University, Port street}
\begin{document}
%
% Add hyperlink to the web location and license of the paper.
% The argument of this command is the handler identifier given
% by the Insight Journal to this paper.
%
\IJhandlefooter{\IJhandlerIDnumber}
\ifpdf
\else
%
% Commands for including Graphics when using latex
%
\DeclareGraphicsExtensions{.eps,.jpg,.gif,.tiff,.bmp,.png}
\DeclareGraphicsRule{.jpg}{eps}{.jpg.bb}{`convert #1 eps:-}
\DeclareGraphicsRule{.gif}{eps}{.gif.bb}{`convert #1 eps:-}
\DeclareGraphicsRule{.tiff}{eps}{.tiff.bb}{`convert #1 eps:-}
\DeclareGraphicsRule{.bmp}{eps}{.bmp.bb}{`convert #1 eps:-}
\DeclareGraphicsRule{.png}{eps}{.png.bb}{`convert #1 eps:-}
\fi
\maketitle
\ifhtml
\chapter*{Front Matter\label{front}}
\fi
% The abstract should be a paragraph or two long, and describe the
% scope of the document.
\begin{abstract}
\noindent
This document describes a new algorithm implemented using the Insight Toolkit
ITK \url{www.itk.org}. The code of the algorithm is written following the
ITK CodingStyle as described in the directory
\code{ITK/Documentation/Style.pdf}
This paper is accompanied with the source code, input data, parameters and
output data that the authors used for validating the algorithm described in
this paper. This adheres to the fundamental principle that scientific
publications must facilitate reproducibility of the reported results.
\end{abstract}
\IJhandlenote{\IJhandlerIDnumber}
\tableofcontents
Using filters from the Insight Toolkit, we develop an algorithm for detecting
and tracking thje movement of solar spots. As it is widely known, celestial
objects such as the sun are ethereal and perfect, and therefore can not harbor
artifacts such as spots. However, observations performed with our open source
telescope have revealed the presence of such spots. The spots seems to continuously change positions on the solar surface.
Automatic detection and tracking of the solar spot movements are of fundamental
importance for allowing the authors to dedicate more time to perfectioning
optical instruments and less time to the supervised acquisition of reliable
data.
The reader should be warned that direct observation of the sun without proper
equipment may result in personal injury, loss of vision and burned brains.
\section{Principles of Solar Spot Detection}
Solar spots can be classified as the darkest objects present on an image of the
solar surface. Algorithms such as watersheds, statistical classification and
mathematical morphology are suitable for automatically detecting these features
in images of the solar surface.
\section{Why Image Processing Papers must include Source Code, Images and Parameters }
Modern Image Processing is most of the time performed with computers. An
attempt to replicate the results of an algorithm described in a paper entails
to reimplement the algorithm into source code. This task is far from trivial
and consumes months of work. The final result can not be guarranted to be
equivalent to the actual code that was used for testing the algorithm when the
paper was written, and therefore it cannot be considered a baseline for
comparing the algoritm with other algorithms availble to the reader.
Papers to the Insight Journal are written in the spirit of facilitating and
encouraging readers to perform replication of work. In this sense, the Insight
Journal is compliant with essential concepts of the scientific method.
Since the code is included with the paper, less time has to be spent in
describing the code, and more time can be used for describing how to use the
algorithm in particular types of images.
For questions on the basis of the scientific method the reader is refered to
\cite{Popper2002,Popper1971}.
\section{Pointing to other material}
The format of this LaTeX file, allows authors to include code snippets, like
the following
\begin{minted}[baselinestretch=1,fontsize=\footnotesize,linenos=false,bgcolor=ltgray]{cpp}
typedef itk::Image< unsigned char, 3 > ImageType;
ImageType::Pointer image = ImageType::New();
\end{minted}
and to cite the online documentation of the Insitght Toolkit, for example, the
link to the doxygen documentation of the ImageToImageFilter
\doxygen{ImageToImageFilter}
LaTeX macros are also available for typesetting code in familiar courier fonts.
Like the following method of an ITK class.
\code{SetNumberOfIterations()}
% The preceding sections will have been written in a gentler,
% introductory style. You may also wish to include a reference
% section, documenting all the functions/exceptions/constants.
% Often, these will be placed in separate files and input like this:
\appendix
\section{This is an Appendix}
To create an appendix in a Insight HOWTO document, use markup like
this:
\begin{verbatim}
\appendix
\section{This is an Appendix}
To create an appendix in a Insight HOWTO document, ....
\section{This is another}
Just add another \section{}, but don't say \appendix again.
\end{verbatim}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Example on how to insert a figure
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{figure}
\center
\includegraphics[width=0.8\textwidth]{Document/LaTeX/RegistrationComponentsDiagram.eps}
\itkcaption[Registration Framework Components]{The basic components of the
registration framework are two input images, a transform, a metric, an
interpolator and an optimizer.}
\label{fig:RegistrationComponents}
\end{figure}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Example on how to insert an equation.
% Never forget to put an equation in your paper.
% They make them look professional and impress the reviewers.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
To support shape-guidance, the generic level set equation
(Eqn(~\ref{eqn:ShapeInfluenceTerm})) is extended to incorporate a shape guidance
term:
\begin{equation}
\label{eqn:ShapeInfluenceTerm}
\xi \left(\psi^{*}(\mathbf{x}) - \psi(\mathbf{x})\right)
\end{equation}
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%
% Insert the bibliography using BibTeX
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\bibliographystyle{plain}
\bibliography{InsightJournal}
\end{document}