1. An Introduction to the LaTex typesetting system LaTeX is a free system for document typesetting. Documents are stored in ASCII text files with markup, macro, tags used to control visual presentation. This separation of content from visual presentation allows users to focus their efforts on improving the quality of the content and only later on addressing the visual aspects of the presentation. LaTex is a highly portable system, both across operating systems and over time, yes, you can easily read LaTex documents written 15 years ago on any operating system you have on your computer today. The system provides high quality typesetting of mathematical equations and graphical representations for a wide variety of disciplines including physics, chemistry, biology, and for the English and music majors there are packages for typesetting poetry and sheet music. In this tutorial we will introduce the structure of a LaTex document, the basic markup macros useful for a scientific publication and the workflow required by the system. Not :

2. An Introduction to the LaTex typesetting system Ziv Yaniv Not : Last Modified October 2011

3. Who (Credit Where Credit is Due) Donald E. Knuth Tex late 70’s Pictures courtesy of wikipedia http://en.wikipedia.org/ LaTex early 80’s Leslie Lamport

4. What A typesetting system, not a word processor. Pronounced “Lay-Tek” or “Lah-Tek”. Tex/LaTex central, Comprehensive TeX Archive Network (CTAN): http://www.ctan.org/http://www.ctan.org/

5. Samples of LaTex All samples taken from: http://www.tug.org/texshowcase/http://www.tug.org/texshowcase/

6. Where to Obtain Win, MikTex: http://www.miktex.org/ http://www.miktex.org/ Unix/Linux, Tex Live: http://tug.org/texlive/ http://tug.org/texlive/ Mac, MacTex: http://tug.org/mactex/ http://tug.org/mactex/

7. Book Recommendation Corner Free online substitutes: The EOS 1918 edition: http://www.crockford.com/wrrrld/style.htmlhttp://www.crockford.com/wrrrld/style.html A (Not So) Short Guide to LaTeX2e : http://www.ctan.org/tex-archive/info/lshort/english/http://www.ctan.org/tex-archive/info/lshort/english/

8. Editors Specifically supporting LaTex Win: WinEdt (shareware), TexnicCenter (freeware). Mac: TexShop Unix/Linux: emacs, Lyx

9. Files Galore *.cls (class file) *.sty (style file) *.bbl (bibliography file) (auxiliary files for system use) *.aux, *.idx, *.toc, *.log *.ps*.pdf *.tex *.dvi

10. Document Structure 1.Preamble 1.document class [article, report, book…], 2.packages [additional macros], 3.your additional macro definitions. 2.Document body.

11. Your First Document

12. Document Body \section{My first section} \subsection{My first subsection} \chapter{My first chapter} \appendix \footnote{My first footnote} \label{firstLabel} \ref{firstLabel} Label-ref mechanism: When using labels and references you will need to run LaTex multiple times (remember those auxiliary files).

13. Your Second Document

14. Basic Formatting force new line and new page: \\ or \newline \newpage bold text: \bf or \textbf{} italicize text: \emph{} or \textit{} or \it underline text: \ul, \underline{} font sizes: \tiny, \scriptsize, \footnotesize, \small, \normalsize, \large, \Large, \LARGE, \huge, \Huge lists: \begin{itemize} \item The first item. \item The second item. \end{itemize} \begin{enumerate} \item The first item. \item The second item. \end{enumerate}

15. Basic Formatting

16. Math Two important packages that add many useful macros: \usepackage{amsmath} \usepackage{amssymb}

17. Math

18. Floating objects (Tables and Figures) Objects that cannot be broken across pages are referred to as floating: –\begin{table} \end{table} –\begin{figure} \end{figure} Table and Figure numbering are done for you. Referencing a floating object is done via the label-ref mechanism. Enhanced support of graphics, add \usepackage{graphicx} in preamble.

19. Floating objects (Tables and Figures)

20. Bibliography Manage bibliography using BibTex program. *.tex*.bib *.bbl In your *.tex file: \bibliographystyle{plain} \bibliography{mybibliography} Bibliography style defined in a ASCII text file (*.bst).

21. Bibliography *.bib file – ASCII text file with entries in a human readable format. Entry types include @article, @book, @inproceedings, @mastersthesis, @techreport…: @ARTICLE{yaniv2010c, author = {Ziv Yaniv}, title = {Evaluation of Spherical Fiducial Localization in {C-arm} Cone-Beam {CT} using Patient Data}, journal = {Med. Phys.}, year = {2010}, volume = {37}, pages = {5298--5305}, number = {10}, } @INPROCEEDINGS{wiesner2007, author = {Stefan Wiesner and Ziv Yaniv}, title = {Monitoring Patient Respiration using a Single Optical Camera}, booktitle = {Int. Conf.of the IEEE Eng. Med. Biol.}, year = {2007}, pages = {2740--2743}, }

22. JabRef GUI for bib file http://jabref.sourceforge.net/

23. LaTex + BibTex To obtain the final typeset file, with all references and citations numbered and in order run the following series of commands: 1.Latex 2.Bibtex 3.Latex 4.Latex

24. LaTex + BibTex @ARTICLE{banovac2005, author = {Filip Banovac and Jonathan Tang and Sheng Xu and David Lindisch and Ho Young Chung and Elliot B. Levy and Thomas Chang and Michael F. McCullough and Ziv Yaniv and Bradford J. Wood and Kevin Cleary}, title = {Precision targeting of liver lesions using a novel electromagnetic navigation device in physiologic phantom and swine}, journal = {Med. Phys.}, year = {2005}, volume = {32}, pages = {2698--2705}, number = {8}, } @ARTICLE{bansal2003, author = {Ravi Bansal and Lawrence H. Staib and Zhe Chen and Anand Rangarajan and Jonathan Knisely and Ravinder Nath and James S. Duncan}, title = {Entropy-Based, Dual-Portal-to-3{DCT} Registration Incorporating Pixel Correlation}, journal = {{IEEE} Trans. Med. Imag.}, year = {2003}, volume = {22}, pages = {29--49}, number = {1}, } @ARTICLE{yaniv2010c, author = {Ziv Yaniv}, title = {Evaluation of Spherical Fiducial Localization in {C-arm} Cone-Beam {CT} using Patient Data}, journal = {Med. Phys.}, year = {2010}, volume = {37}, pages = {5298--5305}, number = {10}, }

25. Bringing It all Together LaTex sources for: "Fiducial localization in C-arm based Cone-Beam CT", Z. Yaniv, SPIE Medical Imaging: Visualization, Image-Guided Procedures, and Display, 2009.

26. Presenting Your Work Embed latex into your power point presentations: 1.Insert formulas as pictures cannot change scale gracefully. 2.Use TexPPT (http://sites.google.com/site/tex4ppt/)http://sites.google.com/site/tex4ppt/ gracefully change scale. copy-paste from the paper you already wrote.

27. Summary This introduction has covered the basic functionality of LaTex and BibTex. These are standard tools in many scientific disciplines. Comprehensive TeX Archive Network (CTAN): http://www.ctan.org/http://www.ctan.org/ Don’t start from scratch, base your documents on previous ones.