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Merge branch 'master' of https://whale.am28.uni-tuebingen.de/git/teaching/scientificComputing

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projects/project_adaptation_fit/adaptation_fit.tex
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\begin{document}
\input{../instructions.tex}
Sensory adaptation is a process that results in a reduced sensitivity of the sensory system to a stimulus. One of the best known examples might be the light adaptation of the eye to constant illumination. The light adaptation that we all know depends on a multitude of processes that regulate the eye sensitivity. Adaptation is not limited to the visual system but is observed even in the responses of individual neurons.
Stimulating a neuron with a constant stimulus for an extended period
of time often results in a decay of an initially strong response. This
process is called adaptation. Your task here is to estimate the
time-constant of the firing-rate adaptation in P-unit electroreceptors
of the weakly electric fish \textit{Apteronotus leptorhynchus}.
of time often results in a decay of an initially strong response. Your task here is to analyze the spike-frequency adaptation observed in the p-type electroreceptor afferents (aka. P-units) in the electrosensory periphery of the
of the weakly electric fish \textit{Apteronotus leptorhynchus}. P-units are driven by the fish's own electric field and changes of field's amplitude leads to a modulation of the cell's firing rate. Extended stimulation with an increased field amplitude allows to observe the exponentially decaying firing rate. While the light adaptation of the human eye is relatively slow, the firing rate adaptation observed in P-units is quite fast. It is your task to estimate how fast it is.
\begin{questions}
\question In the accompanying datasets you find the
\textit{spike\_times} of an P-unit electroreceptor to a stimulus of
a certain intensity, i.e. the \textit{contrast} which is also stored
in the file. The contrast of the stimulus is a measure relative to
the amplitude of fish's field and is given in percent. The data is sampled
the amplitude of fish's own field amplitude and is given in percent. The data is sampled
with 20\,kHz sampling frequency and spike times are given in
milliseconds (not seconds!) relative to stimulus onset.
\begin{parts}

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projects/project_eyetracker/eyetracker.tex
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recorded.
In the accompanying datasets you find a subject's eye tracking data when viewing two different images
(\emph{Genesis\_VIII.png} and \emph{Genesis\_XXXIX.png}, files \verb+1_1.mat+ and \verb+1_2.mat+, respectively). Each \verb+mat+-file contains five variables: \verb+frame_index+, the \verb+gaze_x+ and \verb+gaze_y+ position (in pixel on the screen), a boolean vector \verb+eye_found+ telling whether the tracker could actually estimate the eye position, and a vector \verb+marker+. The \verb+marker+ is used to indicate sections in the data. 0 can be ignored, 1 marks the fixation period and 2 indicates the acutal trial.
(\emph{Genesis\_VIII.png} and \emph{Genesis\_XXXIX.png}, files \verb+1_1.mat+ and \verb+1_2.mat+, respectively). The experiment consisted of different trials. Each trial started with a fixation period, followed by the important free eye-movement part.
Each \verb+mat+-file contains five variables: \verb+frame_index+, the \verb+gaze_x+ and \verb+gaze_y+ position (in pixel on the screen), a boolean vector \verb+eye_found+ telling whether the tracker could actually estimate the eye position, and a vector \verb+marker+. The \verb+marker+ is used to indicate sections in the data. 0 can be ignored, 1 marks the fixation period and 2 indicates the actual trial.
The screen was 37.6\,cm wide and 30.1\,cm high and had a resolution of 1280\,x\,1024\,pixel. The distance between subject's eyes and the screen was 50\,cm.
The eyetracker recorded ey positions with 60\,Hz. The fixation point was shown at the center of the screen and can be used to compensate for possible offests in the \verb+gaze_x+ and \verb+gaze_y+ positions.
@ -30,7 +31,7 @@ The eyetracker recorded ey positions with 60\,Hz. The fixation point was shown a
\question Characterize the eye movements statistically.
\begin{parts}
\part Calculate with eye speed and/or accelerations.
\part Calculate the eye speed and/or accelerations.
\part Create a 'heatmap' plot of the eye-positions.

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projects/project_photoreceptor/photoreceptor.tex
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%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
\section*{Light responses of an insect photoreceptor.}
Fly R\,1--6 photoreceptors respond to light-on stimuli with graded membrane
Insect R\,1--6 photoreceptors respond to light-on stimuli with graded membrane
potential changes. In the acompanying datasets you find the membrane
potential of a single R\,1-6 photoreceptor that was recorded while the receptor was
potential of a single R\,1-6 photoreceptor from the fly \textit{Calliphora vicina}. The receptor was
stimulated with a light stimulus of different amplitudes.
\begin{questions}
\question{} The accompanying dataset (photoreceptor\_data.zip)
contains seven mat files. Each of these holds the data from one
contains seven mat files. Each of these holds the data recorded with one
stimulus intensity and contains three variables. (i)
\textit{voltage} a matrix with the recorded membrane potential from
10 consecutive trials, (ii) \textit{time} a matrix with the