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diff --git a/presentation.pdf b/presentation.pdf
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+++ b/presentation.pdf
diff --git a/presentation.tex b/presentation.tex
index 9f4a3f1..1729bb2 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -1,6 +1,7 @@
 \documentclass{presentation}

 

 \title{Development of \\ Frequency Domain Multidimensional Spectroscopy}

+\subtitle{---Beyond Two Dimensions---}

 \author{Blaise Thompson}

 

 \institute{University of Wisconsin--Madison}

@@ -9,141 +10,137 @@
 \begin{document}

 \maketitle

 

-\section{CMDS}  % =================================================================================

-

-\begin{frame}{CMDS}

-	The Wright Group focuses on the development and usage of \\

-  Coherent MultiDimensional Spectroscopy (CMDS).

-  \vspace{\baselineskip} \\

-  CMDS is a family of related nonlinear spectroscopic experiments.

-\end{frame}

-   

-\begin{frame}{Why CMDS?}

-  [A BUNCH OF COOL PUBLICATIONS---FOCUSING ON COHERENCE TRANSFER, MECHANISMS ETC]

-  [MORE APPLICATIONS]

+\begin{frame}{Brown et al. (1999)}

+  \begin{columns}

+    \begin{column}{0.5\textwidth}

+      \fbox{\adjincludegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a"}}

+    \end{column}

+    \begin{column}{0.5\textwidth}

+      \includegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a_1"}

+      \centering

+      \\

+      \vspace{2\baselineskip}

+      $\vec{k_{\text{sig}}} = \vec{k_a} - \vec{k_b} + \vec{k_c}$

+    \end{column}

+  \end{columns}

 \end{frame}

 

-\begin{frame}{Coherence transfer}

-  \fbox{\adjincludegraphics[width=\textwidth]{literature/ChenuAurelia2014a}}

+\begin{frame}{Overview}

+  \adjincludegraphics[width=\textwidth]{"mixed_domain/simulation overview"}

 \end{frame}

 

-\begin{frame}{Analytical}

-  But wait! I'm an \emph{Analytical} Chemist...

+\begin{frame}{Diversity}

+  Great diversity of experimental strategies.

   \vspace{\baselineskip} \\

-  What am I doing in a field so rich with fundamental studies?

-  \vspace{\baselineskip} \\

-  I hope to convince you that CMDS can be used for analytical work.  % TODO: better

+  Different phase matching conditions...

   \begin{itemize}

-    \item detection (selectivity)

-    \item unknown identification

-    \item quantification

+    \item transient grating $\vec{k_a} - \vec{k_b} + \vec{k_c}$

+    \item transient absorption

+    \item DOVE

+    % TODO: darien's experiments

   \end{itemize}

+  But also different color combinations and dimensions explored.

+  % SAY: based on the same basic ability to scan pulses in frequency, delay etc

 \end{frame}

 

-% TODO: in fact, 2DIR is already used regularly...

-

-\begin{frame}{Pakoulev et al. (2009)}  

-  \fbox{\adjincludegraphics[width=\textwidth]{literature/PakoulevAndreiV2009a}}

+\begin{frame}{MR-CMDS development}

+  [SUMMARY SLIDE FOR REMAINDER OF PRESENTATION]

 \end{frame}

 

-\begin{frame}{Pakoulev et al. (2009)}

-  \begin{shadequote}

-    Spectroscopy forms the heart of the analytical methodology used for routine chemical

-    measurement.  %

-    Of all the analytical spectroscopic methods, NMR spectroscopy is unique in its ability to

-    \hl{correlate} spin resonances and \hl{resolve} spectral features from spectra containing

-    \hl{thousands of peaks}.  %

-    For example, heteronuclear multiple quantum coherence (HMQC) spectroscopy achieves this

-    capability by exciting $^1$H, $^{15}$N, $^{13}$ C=O, and $^{13}$C$\alpha$ spins to form a

-    multiple quantum coherence \hl{characteristic of a specific position} in a protein’s backbone.

-    Three excitations define a specific residue, and a fourth defines the coupling to an adjacent

-    residue.

-    Not only does it decongest the spectra, it defines the couplings and connectivity between the

-    different nuclear spin states.

-    Coherent multidimensional spectroscopy (CMDS) has emerged as the \hl{optical analogue} of

-    nuclear magnetic resonance (NMR), and there is great interest in using it as a \hl{general

-      analytical methodology}.

-  \end{shadequote}

-\end{frame}

+\section{Tunability}  % ===========================================================================

 

-\begin{frame}{Donaldson et al. (2010)}

-  \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}}

+\begin{frame}{Tunability}

+  \centering \huge

+  Control and Calibration of \\

+  Optical Parametric Amplifiers

 \end{frame}

 

-\begin{frame}{Fournier et al. (2009)}

-  \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}}

+\begin{frame}{Two strategies for CMDS}

+  Two strategies for collecting multidimensional spectra:

+  \vspace{\baselineskip} \\

+  \begin{columns}

+    \begin{column}{0.4\textwidth}

+      Time Domain

+      \begin{itemize}

+        \item broadband pulses

+        \item resolve spectra interferometrically

+        \item fast (even single shot)

+        \item robust

+      \end{itemize} 

+    \end{column}

+    \begin{column}{0.4\textwidth}

+      Frequency Domain

+      \begin{itemize}

+        \item narrowband pulses

+        \item resolve spectra by tuning OPAs directly

+        \item slow (lots of motor motion)

+        \item fragile

+      \end{itemize}

+    \end{column}

+  \end{columns}

+\end{frame}

+

+\begin{frame}{Postage stamp}

+  [FIGURE FROM LIT]

+\end{frame}

+

+\begin{frame}{Czech}

+  [FIGURE FROM CZECH]

 \end{frame}

 

-\begin{frame}{Fournier et al. (2009)}

-  \begin{shadequote}

-    Our protein identification strategy is based on using EVV 2DIR to quantify the amino acid

-    content of a protein.  %

-    EVV 2DIR is shown to be able to perform \hl{absolute quantification}, something of major

-    importance in the field of proteomics but rather difficult and time-consuming to achieve with

-    mass spectrometry.  %

-    Our technique can be qualified as a top-down \hl{label-free} method; it does not require

-    intensive sample preparation, the proteins are intact when analyzed, and it does not have any

-    mass restriction on the proteins to be analyzed.  %

-    Moreover, EVV 2DIR is a \hl{nondestructive} technique; the samples can be kept for reanalysis

-    in the light of further information.  %

-  \end{shadequote}

+\begin{frame}{Bandwidth}

+  \adjincludegraphics[width=\textwidth]{opa/OPA_ranges}

 \end{frame}

 

-\section{Frequency domain}  % =====================================================================

-

-\begin{frame}{Domains of CMDS}

-  CMDS can be collected in two domains:

-  \begin{itemize}

-    \item time domain

-    \item frequency domain

-  \end{itemize}

+\begin{frame}{TOPAS-C}

+  \includegraphics[width=\textwidth]{opa/TOPAS-C}

+  Two ``stages'', each with two motorized optics.

 \end{frame}

 

-\begin{frame}{Time domain}

-  Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram

-  (analogous to FTIR, NMR).

+\begin{frame}{Tuning}

+  % TODO: curve plot?

+  Tuning curves---recorded correspondence between motor positions and output color.

   \vspace{\baselineskip} \\

-  A local oscillator must be used to measure the \emph{phase} of the output.

+  Exquisite sensitivity to alignment and lab conditions---tuning required roughly once a week.

   \vspace{\baselineskip} \\

-  This technique is...

+  Manual tuning is difficult...

   \begin{itemize}

-    \item fast (even single shot)

-    \item robust

+    \item high dimensional motor space

+    \item difficult to asses overall quality

+    \item several hours of work per OPA (sometimes, an entire day for one OPA)

   \end{itemize}

-  pulse shapers have made time-domain CMDS (2DIR) almost routine.

 \end{frame}

 

-\begin{frame}{Frequency domain}

-  In the Wright Group, we focus on \emph{frequency} domain ``Multi-Resonant'' (MR)-CMDS.

-  \vspace{\baselineskip} \\

-  Automated Optical Parametric Amplifiers (OPAs) are used to produce relatively narrow-band pulses.

-  Multidimensional spectra are collected ``directly'' by scanning OPAs against each-other.

-  \vspace{\baselineskip} \\

-  This strategy is...

-  \begin{itemize}

-    \item slow (must directly visit each pixel)

-    \item fragile (many crucial moving pieces)

-  \end{itemize}

-  but! It is incredibly flexible.  

+\begin{frame}{Preamp}

+  \includegraphics[width=\textwidth]{opa/preamp}

 \end{frame}

 

-\begin{frame}{Bandwidth}

-  MR-CMDS has no bandwidth limit!

-  \vspace{\baselineskip} \\

-  There is just the small matter of making the source continuously tunable...

-  \adjincludegraphics[width=\textwidth]{opa/OPA_ranges}

+\begin{frame}{Automation}

+  \begin{columns}

+    \begin{column}{0.5\textwidth}

+      \adjincludegraphics[width=\textwidth]{opa/autotune_preamp}

+    \end{column}

+    \begin{column}{0.5\textwidth}

+      Fully automated OPA tuning

+      \begin{itemize}

+        \item less than 1 hour per OPA

+        \item can be scheduled for odd times

+        \item high quality from global analysis 

+        \item reproducible

+        \item unambiguous representations

+      \end{itemize}

+      \vspace{\baselineskip} \\

+      Other calibration steps also automated.

+    \end{column}

+  \end{columns}

 \end{frame}

 

-\begin{frame}{Selection rules}

-  MR-CMDS can easily collect data without an external local oscillator.

-  \vspace{\baselineskip} \\

-  This means... [BOYLE]

-\end{frame}

-

-\section{The instrument}  % =======================================================================

+\section{Acquisition}  % ==========================================================================

 

-\begin{frame}{The instrument}

-  [PICTURE OF LASER LAB]

+\begin{frame}{Acquisition}

+  \centering \huge

+  Control of the MR-CMDS \\

+  Instrument

 \end{frame}

 

 \begin{frame}{The instrument}

@@ -166,33 +163,6 @@
   How to increase data throughput and quality, while decreasing frustration of experimentalists?  %

 \end{frame}

 

-\section{Processing}  % ===========================================================================

-

-\begin{frame}{Processing}

-  WrightTools.

-\end{frame}

-

-\begin{frame}{Universal format}

-  WrightTools defines a \emph{universal file format} for CMDS.

-  \begin{itemize}

-    \item store multiple multidimensional arrays

-    \item metadata

-  \end{itemize}

-  Import data from a variety of sources.

-  \begin{itemize}

-    \item previous Wright Group acquisition software

-    \item commercial instruments (JASCO, Shimadzu, Ocean Optics)

-  \end{itemize}

-\end{frame}

-

-\begin{frame}{Flexible data model}

-  Flexibility to transform into any desired ``projection'' on component variables.

-  \adjincludegraphics[width=\textwidth]{processing/fringes_transform}

-  % mention: including expressions

-\end{frame}

-

-\section{Acquisition}  % ==========================================================================

-

 \begin{frame}{Acquisition}

   PyCMDS---unified software for controlling hardware and collecting data.

   \adjincludegraphics[width=\textwidth]{acquisition/screenshots/000}

@@ -203,18 +173,6 @@
   \vspace{\baselineskip} \\

   Sensor---something that has a \hl{signal} that can be \hl{read}.

 \end{frame}

-  

-\begin{frame}{Modular hardware model}

-  \adjincludegraphics[scale=0.25]{acquisition/hardware_inheritance}

-\end{frame}

-

-\begin{frame}{Modular sensor model}

-  Can have as many sensors as needed.

-  \vspace{\baselineskip} \\

-  Each sensor contributes one or more channels.

-  \vspace{\baselineskip} \\

-  Sensors with size contribute new variables (dimensions).

-\end{frame}

 

 \begin{frame}{Central loop}

   Set, wait, read, wait, repeat.

@@ -241,9 +199,25 @@
   \end{itemize}

 \end{frame}

 

-\section{Tuning}  % ===============================================================================

+\subsection{Extensibility}  % ---------------------------------------------------------------------

 

-\begin{frame}{Tuning}

+% DARIEN ADDED AEROTECH STAGE---1 DAY

+

+% SUNDEN ADDED CUSTOM POYNTING TUNE IN A FEW DAYS (including testing)

+

+\section{Processing}  % ===========================================================================

+

+\begin{frame}{Processing}

+  WrightTools.

+\end{frame}

+

+\begin{frame}{TOC}

+\end{frame}

+

+\begin{frame}{Flexible data model}

+  Flexibility to transform into any desired ``projection'' on component variables.

+  \adjincludegraphics[width=\textwidth]{processing/fringes_transform}

+  % mention: including expressions

 \end{frame}

 

 \section{Conclusion}  % ===========================================================================

@@ -252,6 +226,73 @@
 \end{frame}

 

 \section{Supplement}  % ===========================================================================

+ 

+\begin{frame}{Modular hardware model}

+  \adjincludegraphics[scale=0.25]{acquisition/hardware_inheritance}

+\end{frame}

+

+\begin{frame}{Modular sensor model}

+  Can have as many sensors as needed.

+  \vspace{\baselineskip} \\

+  Each sensor contributes one or more channels.

+  \vspace{\baselineskip} \\

+  Sensors with size contribute new variables (dimensions).

+\end{frame}

+

+\begin{frame}{Universal format}

+  WrightTools defines a \emph{universal file format} for CMDS.

+  \begin{itemize}

+    \item store multiple multidimensional arrays

+    \item metadata

+  \end{itemize}

+  Import data from a variety of sources.

+  \begin{itemize}

+    \item previous Wright Group acquisition software

+    \item commercial instruments (JASCO, Shimadzu, Ocean Optics)

+  \end{itemize}

+\end{frame}

+

+\begin{frame}{Domains of CMDS}

+  CMDS can be collected in two domains:

+  \begin{itemize}

+    \item time domain

+    \item frequency domain

+  \end{itemize}

+\end{frame}

+

+\begin{frame}{Time domain}

+  Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram

+  (analogous to FTIR, NMR).

+  \vspace{\baselineskip} \\

+  A local oscillator must be used to measure the \emph{phase} of the output.

+  \vspace{\baselineskip} \\

+  This technique is...

+  \begin{itemize}

+    \item fast (even single shot)

+    \item robust

+  \end{itemize}

+  pulse shapers have made time-domain CMDS (2DIR) almost routine.

+\end{frame}

+

+\begin{frame}{Frequency domain}

+  In the Wright Group, we focus on \emph{frequency} domain ``Multi-Resonant'' (MR)-CMDS.

+  \vspace{\baselineskip} \\

+  Automated Optical Parametric Amplifiers (OPAs) are used to produce relatively narrow-band pulses.

+  Multidimensional spectra are collected ``directly'' by scanning OPAs against each-other.

+  \vspace{\baselineskip} \\

+  This strategy is...

+  \begin{itemize}

+    \item slow (must directly visit each pixel)

+    \item fragile (many crucial moving pieces)

+  \end{itemize}

+  but! It is incredibly flexible.  

+\end{frame}

+

+\begin{frame}{Selection rules}

+  MR-CMDS can easily collect data without an external local oscillator.

+  \vspace{\baselineskip} \\

+  This means... [BOYLE]

+\end{frame}

 

 \begin{frame}{MR-CMDS theory}

 \end{frame}