diff --git a/projects/disclaimer.tex b/projects/disclaimer.tex index 4e1b7dd..6397967 100644 --- a/projects/disclaimer.tex +++ b/projects/disclaimer.tex @@ -8,26 +8,28 @@ \vspace{1ex} The {\bf code} and the {\bf presentation} should be uploaded to - ILIAS at latest on Thursday, November 6th, 10:00h. - The presentations start on Thursday 11:00h. Please hand in - your presentation as a pdf file. Bundle everything into a - {\em single} zip-file. + ILIAS at latest on Thursday, November 5th, 13:00h. The + presentations start on Thursday 13:00h. Please hand in your + presentation as a pdf file. Bundle everything (the pdf and the + code) into a {\em single} zip-file. \vspace{1ex} The {\bf code} should be exectuable without any further - adjustments from us. This means that you need to include all + adjustments from our side. This means that you need to include all additional functions you wrote and the data into the - zip-file. A single {\em main script} should produce the same + zip-file. A single {\em main} script should produce the same {\em figures} that you use in your slides. The figures should follow the guidelines for proper plotting as discussed in the - first statistics lecture. The code should be properly commented + course. The code should be properly commented and comprehensible by third persons (use proper and consistent - variable names). + variable and function names). \vspace{1ex} \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. + number as a comment at the top of a script called + \texttt{main.m}.} The \texttt{main.m} script then should + coordinate the execution of your analysis by e.g. calling + sub-scripts and functions with appropriate parameters. \vspace{1ex} diff --git a/projects/project_adaptation_fit/adaptation_fit.tex b/projects/project_adaptation_fit/adaptation_fit.tex index f5e4ca8..c9b6af0 100644 --- a/projects/project_adaptation_fit/adaptation_fit.tex +++ b/projects/project_adaptation_fit/adaptation_fit.tex @@ -6,8 +6,8 @@ \pagestyle{headandfoot} \runningheadrule \firstpageheadrule -\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 - -- 11/06/2014} +\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2015 + -- 11/05/2015} %\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} \firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe} \runningfooter{}{}{} @@ -44,15 +44,14 @@ electroreceptors of the weakly electric fish \textit{Apteronotus certain intensity, i.e. the \textit{contrast} which is also stored in the file. \begin{parts} - \part Estimate for each stimulus intensity the - PSTH and plot it. You will see that there are three parts. (i) - The first 200 ms is the baseline (no stimulus) activity. (ii) - During the next 1000 ms the stimulus was switched on. (iii) After - stimulus offset the neuronal activity was recorded for further 825 - ms. - \part Estimate the adaptation time-constant of the adaptation for - both the stimulus on- and offset. To do this fit an exponential - function to the data. For the decay use: + \part Estimate for each stimulus intensity the PSTH and plot + it. You will see that there are three parts. (i) The first + 200\,ms is the baseline (no stimulus) activity. (ii) During the + next 1000\,ms the stimulus was switched on. (iii) After stimulus + offset the neuronal activity was recorded for further 825\,ms. + \part Estimate the adaptation time-constant for both the stimulus + on- and offset. To do this fit an exponential function to the + data. For the decay use: \begin{equation} f_{A,\tau,y_0}(t) = y_0 + A \cdot e^{-\frac{t}{\tau}}, \end{equation} @@ -62,7 +61,7 @@ electroreceptors of the weakly electric fish \textit{Apteronotus \begin{equation} f_{A,\tau, y_0}(t) = y_0 + A \cdot \left(1 - e^{-\frac{t}{\tau}}\right ), \end{equation} - \part Plot the decays into the data. + \part Plot the best fits into the data. \part Plot the estimated time-constants as a function of stimulus intensity. \end{parts} \end{questions} diff --git a/projects/project_eod/eod.tex b/projects/project_eod/eod.tex index f814ffe..cb9bc23 100644 --- a/projects/project_eod/eod.tex +++ b/projects/project_eod/eod.tex @@ -6,10 +6,10 @@ \pagestyle{headandfoot} \runningheadrule \firstpageheadrule -\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 - -- 11/06/2014} +\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2015 + -- 11/05/2015} %\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} -\firstpagefooter{}{}{{\bf Supervisor:} Fabian Sinz} +\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe} \runningfooter{}{}{} \pointsinmargin \bracketedpoints @@ -38,8 +38,9 @@ \begin{parts} \part Load and plot the data in an appropriate way. Time is in seconds and the voltage is in mV/cm. - \part Fit the following curve to the eod (select a smaller time - window for fitting, not the entire trace) using least squares: + \part Fit the following curve to the eod (select a small time + window, a few tens of milliseconds, for fitting, not the entire + trace) using least squares: $$f_{\omega_0,b_0,\varphi_1, ...,\varphi_n}(t) = b_0 + \sum_{j=1}^n \sin(2\pi j\omega_0\cdot t + \varphi_j ).$$ $\omega_0$ is called {\em fundamental frequency}. The single terms diff --git a/projects/project_numbers/numbers.tex b/projects/project_numbers/numbers.tex index 7ed8c44..6783598 100644 --- a/projects/project_numbers/numbers.tex +++ b/projects/project_numbers/numbers.tex @@ -6,10 +6,10 @@ \pagestyle{headandfoot} \runningheadrule \firstpageheadrule -\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 - -- 11/06/2014} +\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2015 + -- 11/05/2015} %\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} -\firstpagefooter{}{}{{\bf Supervisor:} Fabian Sinz} +\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe} \runningfooter{}{}{} \pointsinmargin \bracketedpoints @@ -37,24 +37,20 @@ macaque prefrontal cortex (data courtesy of Prof. Nieder). The task of the monkey was to discriminate point-sets with 1 to 4 points. The first column contains the number of points shown plus one. The - remaining columns contain the spike response across 1300ms. During - the first 500ms the monkey was fixating a target. The next 800ms the - stimulus was shown. This was followed by 1000ms delay time before + remaining columns contain the spike response across 1300\,ms. During + the first 500\,ms the monkey was fixating a target. The next 800\,ms the + stimulus was shown. This was followed by 1000\,ms delay time before the monkey was allowed to respond. \begin{parts} \part Plot the data in an appropriate way. \part Sort the trials according to the stimulus presented and compute the firing rate (in Hz) in the time interval - 500-1300ms. Plot the firing rate in an appropriate way. + 500-1300\,ms. Plot the firing rate in an appropriate way. \part Use an appropriate test to determine whether the firing rate in that interval is significantly different for 1 vs. 4 points shown. \end{parts} \end{questions} - - - - \end{document} diff --git a/projects/project_onset_fi/onset_fi.tex b/projects/project_onset_fi/onset_fi.tex index 0954e34..b454a25 100644 --- a/projects/project_onset_fi/onset_fi.tex +++ b/projects/project_onset_fi/onset_fi.tex @@ -6,8 +6,8 @@ \pagestyle{headandfoot} \runningheadrule \firstpageheadrule -\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 - -- 11/06/2014} +\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2015 + -- 11/05/2015} %\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} \firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe} \runningfooter{}{}{} @@ -37,19 +37,19 @@ of the stimulus \textbf{I}ntensity. \begin{questions} \question In the accompanying datasets you find the - \textit{spike\_times} of an P-unit electrorecptor of the weakly + \textit{spike\_times} of an P-unit electroreceptor of the weakly electric fish \textit{Apteronotus leptorhynchus} to a stimulus of a certain intensity, i.e. the \textit{contrast}. \begin{parts} \part For each stimulus intensity estimate the average response (PSTH) and plot it. You will see that there are three parts. (i) - The first 200 ms is the baseline (no stimulus) activity. (ii) - During the next 1000 ms the stimulus was switched on. (iii) After - stimulus offset the neuronal activity was recorded for further 825 - ms. - \part Extract the neuron's activity in the first 50 ms after stimulus onset - and plot it against the stimulus intensity, respectively the - contrast, in an appropriate way. + The first 200\,ms is the baseline (no stimulus) activity. (ii) + During the next 1000\,ms the stimulus was switched on. (iii) After + stimulus offset the neuronal activity was recorded for further + 825\,ms. + \part Extract the neuron's activity in the first 50\,ms after + stimulus onset and plot it against the stimulus intensity, + respectively the contrast, in an appropriate way. \part Fit a Boltzmann function to the FI-curve. The Boltzmann function is defined as: \begin{equation} @@ -62,8 +62,4 @@ of the stimulus \textbf{I}ntensity. \end{parts} \end{questions} - - - - \end{document} diff --git a/projects/project_stimulus_reconstruction/stimulus_reconstruction.tex b/projects/project_stimulus_reconstruction/stimulus_reconstruction.tex index d2a7e14..1ac3390 100644 --- a/projects/project_stimulus_reconstruction/stimulus_reconstruction.tex +++ b/projects/project_stimulus_reconstruction/stimulus_reconstruction.tex @@ -6,8 +6,8 @@ \pagestyle{headandfoot} \runningheadrule \firstpageheadrule -\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 - -- 11/06/2014} +\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2015 + -- 11/05/2015} %\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} \firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe} \runningfooter{}{}{} @@ -31,8 +31,16 @@ %%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%% \section*{Reverse reconstruction of the stimulus evoking neuronal responses.} -During the course we have used the Spike-Triggered-Average to +To analyse encoding properties of a neuron one often calculates the +Spike-Triggered-Average (STA). +\[ STA(\tau) = \frac{1}{\langle n \rangle} \left\langle + \displaystyle\sum_{i=1}^{n}{s(t_i - \tau)} \right\rangle \] + +The STA is the average stimulus that led to a spike in the neuron and +can calculated by cutting out snippets form the stimulus centered on +the respective spike time. The Spike-Triggered-Average can be used to reconstruct the stimulus a neuron has been stimulated with. + \begin{questions} \question In the accompanying files you find the spike responses of P-units and pyramidal neurons of the weakly electric fish diff --git a/projects/project_vector_strength/vector_strength.tex b/projects/project_vector_strength/vector_strength.tex index a56e789..a98bb46 100755 --- a/projects/project_vector_strength/vector_strength.tex +++ b/projects/project_vector_strength/vector_strength.tex @@ -6,8 +6,8 @@ \pagestyle{headandfoot} \runningheadrule \firstpageheadrule -\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 - -- 11/06/2014} +\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2015 + -- 11/05/2015} %\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} \firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe} \runningfooter{}{}{} @@ -31,7 +31,7 @@ %%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%% \section*{Quantifying the coupling of action potentials to the EOD.} -P-unit electrorecptors are driven by the fish's self-generated field, +P-unit electroreceptors are driven by the fish's self-generated field, the EOD. In this project you have to quantify the strength of this coulpling using the \textbf{vector strength}: \begin{equation} @@ -46,7 +46,7 @@ locking, respectively. \begin{questions} \question In the accompanying datasets you find recrordings of the - ``baseline'' activity of P-unit electrorecptors of different weakly + ``baseline'' activity of P-unit electroreceptors of different weakly electric fish of the species \textit{Apteronotus leptorhynchus}. The files further contain respective recordings of the \textit{eod}, i.e. the fish's field.