Tweaked formatting of handout. Improved description in section 3

handout/Ca_Imaging_Analysis.tex

@@ -7,7 +7,7 @@
 \usepackage[T1]{fontenc} % Use 8-bit encoding that has 256 glyphs
 \renewcommand{\familydefault}{\sfdefault}
 \usepackage{fullpage}
-\usepackage{helvet}
+\usepackage{helvet, mathptmx}
 \usepackage[compact,pagestyles]{titlesec}
 \titlespacing\subsection{0pt}{12pt plus 4pt minus 2pt}{0pt plus 0pt minus 5pt}
 \usepackage[english]{babel} % English language/hyphenation
@@ -17,6 +17,8 @@
 \usepackage{graphicx,caption,subcaption}
 \usepackage{todonotes}
 \setlength{\parskip}{18pt}
+\widowpenalty10000
+\clubpenalty10000
 
 \numberwithin{equation}{section} % Number equations within sections (i.e. 1.1, 1.2, 2.1, 2.2 instead of 1, 2, 3, 4)
 \numberwithin{figure}{section} % Number figures within sections (i.e. 1.1, 1.2, 2.1, 2.2 instead of 1, 2, 3, 4)
@@ -89,17 +91,39 @@ \subsection*{Start MATLAB and download the data}
 
 \section{Extract response time-course from a cell}
 
+\begin{figure}[h]
+    \centering
+    \begin{subfigure}[b]{0.3\textwidth}
+    \includegraphics[width=\textwidth]{mean_image.pdf}
+    \caption{Mean projection}
+    \label{fig:mean_ca}
+    \end{subfigure}
+    \hfill
+    \begin{subfigure}[b]{0.3\textwidth}
+    \includegraphics[width=\textwidth]{trace_raw.pdf}
+    \caption{Raw fluorescence trace}
+    \label{fig:time_trace}
+    \end{subfigure}
+    \hfill
+    \begin{subfigure}[b]{0.3\textwidth}
+    \includegraphics[width=\textwidth]{trace_delta_f_f0.pdf}
+    \caption{$\Delta F/F_0$ time trace}
+    \label{fig:time_trace_dff0}
+    \end{subfigure}
+    \caption{By the end of this Section you should have obtained plots that look something like these}
+\end{figure}
+
 First, you will load images, select a cell and display its raw response trace:
 
 \begin{itemize}
 \item Load the image stack called \texttt{Calcium\_imaging\_data\_int8.tif} using the provided \texttt{load\_stack} function.
   Do not forget to use \texttt{help load\_stack} to see how to use this function.
-\item What is the size of the loaded stack (image width and height in pixels, number of frames)? \textbf{Write} down your answer.
-  \vspace{1em}
+\item What is the size of the loaded stack (image width and height in pixels, number of frames)? \textbf{Write} down your answer:
+  \vspace*{0.75in}
 \item Open the provided file \texttt{calc\_mean.m} in the ``to\_be\_completed'' directory. \textbf{Edit} it to calculate the average image: use the \texttt{mean} function and assign the result to a variable called \texttt{meanIM}. Use this function to calculate the average image of the loaded stack.
 \item Plot the image using the \texttt{imagesc} function (see Figure~\ref{fig:mean_ca}). \textbf{Save} your image in \emph{to\_be\_completed} as ``meanImage.png''
 \item Look at the image. What does this tell you about the activity of different neurons? \textbf{Write} down your answer:
-  \vspace{2em}
+  \vspace*{1in}
 \item Start the ROI (Region of Interest) selection GUI using the function \texttt{get\_roi\_trace}. 
 See \texttt{help get\_roi\_trace} if you are unsure of the input arguments.
 On the new figure, draw an ellipse around a cell to highlight it. Double-click on the ellipse, and the average time-trace of the pixels within your ROI will be returned.
@@ -116,28 +140,6 @@ \section{Extract response time-course from a cell}
 \item Run your \texttt{calc\_dF\_F.m} function on the raw trace and plot the $dF/F$ using \texttt{plot} (see Figure~\ref{fig:time_trace_dff0}). \textbf{Save} your image as ``dffTrace.png''.
 \end{itemize}
 
-\begin{figure}
-    \centering
-    \begin{subfigure}[b]{0.3\textwidth}
-    \includegraphics[width=\textwidth]{mean_image.pdf}
-    \caption{Mean projection}
-    \label{fig:mean_ca}
-    \end{subfigure}
-    \hfill
-    \begin{subfigure}[b]{0.3\textwidth}
-    \includegraphics[width=\textwidth]{trace_raw.pdf}
-    \caption{Raw fluorescence trace}
-    \label{fig:time_trace}
-    \end{subfigure}
-    \hfill
-    \begin{subfigure}[b]{0.3\textwidth}
-    \includegraphics[width=\textwidth]{trace_delta_f_f0.pdf}
-    \caption{$\Delta F/F_0$ time trace}
-    \label{fig:time_trace_dff0}
-    \end{subfigure}
-    \caption{By the end of this Section you should have obtained plots that look something like these}
-\end{figure}
-
 
 \section{Understanding the stimulus presentation paradigm}
 
@@ -146,19 +148,10 @@ \section{Understanding the stimulus presentation paradigm}
 
 \begin{itemize}
 \item \textbf{Draw} below what this stimulation paradigm looks like over time, by indicating the time in seconds for baseline and for stimulus presentation, for a single presentation of a drafting grating.
-  \vspace{2.5in}
-\item How many frames are in one stimulus presentation (blank+stim)? What is the imaging frame rate? \textbf{Write} down your answers and \textbf{add} the number of frames on your drawing above.
-\item The drift direction in degrees presented for each stimulus frame is saved in the file \texttt{ori\_stimuli.mat}.
-  Load these data using the \texttt{load} function. What is the name of the variable containing the orientation information (look at the work space)?
-  Use the \texttt{plot} command to look at the contents of this variable. What do you notice about the order in which the stimuli are presented? 
-  \textbf{Write} your answer:\\
-  \vspace{2in}
-\item Open the provided file \texttt{meanTraces.m}. This function will be used to split up the response into presentations of the same directions, over the three trials per direction, and average over trials. \textbf{Complete} the file \texttt{meanTraces.m}. Pay attention to the comments in the file.
-\item Your \texttt{meanTraces} function averages the three individual trial traces for each direction. 
- Plot these average traces for each of the 16 stimulus directions on the same plot (see Figure~\ref{fig:trace_all_ori}). \textbf{Save} your image as ``meanTraces.png''
-\item Plot a single average trace over all stimuli. Where does the peak fall with respect to the stimulus start time? Refer to your diagram, above.
+  \vspace*{2.5in}
 \end{itemize}
 
+
 \begin{figure}
     \centering
     \begin{subfigure}[b]{0.46\textwidth}
@@ -175,6 +168,21 @@ \section{Understanding the stimulus presentation paradigm}
     \caption{}
 \end{figure}
 
+\begin{itemize}
+\item How many frames are in one stimulus presentation (blank+stim)? What is the imaging frame rate? \textbf{Write} down your answers and \textbf{add} the number of frames on your drawing from the last question.
+	\vspace*{1in}
+\item The drift direction in degrees presented for each stimulus frame is saved in the file \texttt{ori\_stimuli.mat}.
+  Load these data using the \texttt{load} function. What is the name of the variable containing the orientation information (look at the work space)?
+  Use the \texttt{plot} command to look at the contents of this variable. What do you notice about the order in which the stimuli are presented? 
+  \textbf{Write} your answers:\\
+  \vspace{2in}
+\item Open the provided file \texttt{meanTraces.m}. This function will be used to split up the response into presentations of the same directions, over the three trials per direction, and average over trials. \textbf{Complete} the file \texttt{meanTraces.m}. Pay attention to the comments in the file.
+\item Your \texttt{meanTraces} function averages the three individual trial traces for each direction. 
+ Plot these average traces for each of the 16 stimulus directions on the same plot (see Figure~\ref{fig:trace_all_ori}). \textbf{Save} your image as ``meanTraces.png''.
+\item Plot a single average trace over all stimuli. Where does the peak fall with respect to the stimulus start time? Refer to your diagram, above.
+\end{itemize}
+
+
 
 \section{Calculate responses to different stimuli}
 
@@ -184,16 +192,16 @@ \section{Calculate responses to different stimuli}
 \item Open the file \texttt{makePolarPlot.m}. This function will be used to display the mean response for each orientation.
   \textbf{Edit} the function as follows:
   \begin{enumerate}
-  \item Choose a window of 5 time points that should contain the peak response to a stimulus, during the stimulus period.
+  \item Choose a window of 5 time points (i.e. 5 frame indices) that should contain the peak response to a stimulus, during the stimulus period.
   \item Average the 5 time points within this window, from the average timecourse of each stimulus orientation.
   \item Plot the mean responses on a polar plot, which will reveal the orientation tuning of the cell, using the \texttt{polar} function (see Figure~\ref{fig:polar_ori_plot}).
   \end{enumerate}
-\item Why is a polar plot a better choice than a conventional x/y line or scatter plot? \textbf{Write} down your answer.
-  \vspace{1em}
+\item Why is a polar plot a better choice than a conventional x/y line or scatter plot? \textbf{Write} down your answer:
+  \vspace*{1in}
 \item Use the \texttt{makePolarPlot} function to plot the preferred orientation(s) of your cell. \textbf{Save} your image as ``polarResult.png''.
 \item Is your cell tuned to the drift direction of the stimulus? Is your cell tuned to the drift direction of two stimuli of the same orientation?
-  \textbf{Write} down your answer.
-  \vspace{2em}
+  \textbf{Write} down your answer:
+  \vspace*{1in}
 \end{itemize}
 
 To assess the selectivity of your cell, you will compute its \emph{orientation selectivity index} (OSI).