Merge branch 'master' of raven:scientificComputing

programming/lectures/sta_stc.tex

@@ -99,14 +99,6 @@ Cross-Correlation, Spike--Triggered--Average and Reverse Reconstruction}
 \end{frame}
 
 
-\begin{frame}[plain]
-  \frametitle{Rekapitulation}
-  \begin{enumerate}
-  \item PSTH\pause
-  \end{enumerate}
-\end{frame}
-
-
 \begin{frame}
   \frametitle{Introduction to scientific computing}
   \frametitle{Menue}
@@ -119,7 +111,7 @@ Cross-Correlation, Spike--Triggered--Average and Reverse Reconstruction}
 
 
 \begin{frame}[plain]
-  \huge{1. Recapitulation: PSTH}
+  \huge{1. Recapitulation: Plotting neuronal activity as a function of time.}
 \end{frame}
 
 
@@ -142,6 +134,17 @@ Cross-Correlation, Spike--Triggered--Average and Reverse Reconstruction}
 \end{frame}
 
 
+\begin{frame}
+  \frametitle{Relating stimulus and response}
+  \framesubtitle{Displaying the neuronal response over time - PSTH}
+  \begin{itemize}
+  \item What does this tell us? \pause
+  \item Wouldn't it be more interesting to relate the response to the stimulus?!
+  \end{itemize}
+\end{frame}
+
+
+
 \begin{frame}[plain]
   \huge{2. Relating stimulus and response}
 \end{frame}
@@ -152,7 +155,7 @@ Cross-Correlation, Spike--Triggered--Average and Reverse Reconstruction}
   \framesubtitle{How can we relate the response to the stimulus?}
     \begin{figure}
       \centering
-      \includegraphics[height=0.9\textheight]{images/conv_stim}
+      \includegraphics[height=0.75\textheight]{images/conv_stim}
     \end{figure}
 \end{frame}
 
@@ -201,20 +204,34 @@ ylabel('correlation')
   \frametitle{Relating stimulus and response}
   \framesubtitle{Cross--correlation - Exercises} 
   \begin{enumerate}
-  \item calculate the cross-correlation between two vectors of random
+  \item Calculate the cross-correlation between two vectors of random
     numbers.
   \item Calculate the cross-correlation between one of these vectors
     and itself (auto-correlation).
   \item Calculate the cross-correlation between one vector and a
     time-shifted version of itself (use \verb+circshift+ to do this).
+  \item Generate two vectors of random numbers, one having a (slight)
+    correlation with the other.
+  \item Calculate the correlation coefficient (\verb+corrcoef+).
+  \item Calculate the cross-correlation.
+  \item Calculate the the correlation coefficient between the one
+    vector and a \verb+circshif+ted version of the other.
+  \item Calculate the cross-correlation of these.
+  \item Find out the maximum correlation and its position.
   \end{enumerate}
   \textbf{Note:} Select max\_lag to be less than 10\% of the length of
   your vectors!
+\end{frame}
+
+
+\begin{frame}[fagile]
+  \frametitle{Relating stimulus and response}
+  \framesubtitle{Cross--correlation - Exercises} 
   \begin{enumerate}
   \item Create the cross correlation of the p-unit data and stimulus.
   \item \textbf{Note:} you have to convert the spike\_times to a PSTH!
   \item Find out the position of the correlation peak. 
-  \item What does this tell you?
+  \item What does it tell you?
   \end{enumerate}
 \end{frame}
 
@@ -273,8 +290,8 @@ ylabel('correlation')
   \begin{enumerate}
     \item Write a function \verb+sta(x, y, count, sample_rate)+ that
       takes the stimulus (x), the response (y, as spike times), the
-      number (count) of sampling points it should cut out from the
+      number (count) of sample points it should cut out from the
-      stimulus and the sampling\_rate to convert from times to
+      stimulus and the sample\_rate to convert from times to
       indices.
     \item \textbf{Beware:} sometimes the spike\_time may be too close
       to the beginning or the end of the stimulus to cut out enough
@@ -284,23 +301,6 @@ ylabel('correlation')
 \end{frame}
 
 
-\begin{frame}[fragile]
-  \frametitle{Relating stimulus and response}
-  \framesubtitle{Spike--Triggered--Average -- STA}
-  What does the \textbf{STA} tell us?
-  \begin{figure}
-    \centering
-    \includegraphics[width=0.25\columnwidth]{images/sta}
-  \end{figure}
-  \begin{enumerate}
-  \item Is there a relation between stimulus and response?\pause
-  \item Is there a lag between them and how large is it?\pause
-  \item How far in the past does a neuron encode?\pause
-  \item Can it see into the future?
-  \end{enumerate}
-\end{frame}
-
-
 \begin{frame}[plain]
   \huge{3. Reverse reconstruction using the \textbf{STA}}
 \end{frame}

projects/disclaimer.tex

@@ -8,30 +8,34 @@
       \vspace{.5cm}
 
       The {\bf code} and the {\bf presentation} should be uploaded to
-      ILIAS before the presentations start on Thursday. Everything
+      ILIAS at latest on Thursday, November 6th, 12:00h.
-      should be bundeled into a {\em single} zip-file. The
+      The presentations start on Thursday 13:00h. Please hand in
-      presentation should be handed in as pdf.
+      your presentation as a pdf file. Bundle everything into a
+      {\em single} zip-file.
 
       \vspace{.5cm}
 
       The {\bf code} should be exectuable without any further
-      adjustments from us. This means that you should include all
+      adjustments from us. This means that you need to include all
       additional functions you wrote and the data into the
-      zip-file. The {\em main script} should produce the same {\em
+      zip-file. A single {\em main script} should produce the same
-      figures} that you use in your slides. The figures should follow
+      {\em figures} that you use in your slides. The figures should
-      the guidelines for proper plotting as discussed in the first
+      follow the guidelines for proper plotting as discussed in the
-      statistics lecture. The code should be properly commented and
+      first statistics lecture. The code should be properly commented
-      comprehensible by third persons (use proper and consistent
+      and comprehensible by third persons (use proper and consistent
       variable names).
 
+      \vspace{.5cm} \textbf{Please write your name and matriculation
+      number as a comment at the top of a script called \texttt{main.m}!}
+      The \texttt{main.m} script then should call all your scripts.
+
       \vspace{.5cm}
       
-      The {\bf slides} should be handed in along with the code and in
+      The {\bf presentation} should be {\em at most} 10min long and be
-      pdf format. We will store them all on one computer to allow fast
+      held in English. In the presentation you should (i) briefly
-      transitions between talks. The {\bf presentation} itself should
+      describe the problem, (ii) explain how you solved it
-      be {\em at most} 10min long and be held in English. In the
+      algorithmically (don't show your entire code), and (iii) present
-      presentation you should (i) briefly describe the problem, (ii)
+      figures showing your results. We will store all presentations on
-      explain how you solved it algorithmically (don't show your
+      one computer to allow fast transitions between talks.
-      entire code), and (iii) present figures showing your results. 
 
     }}