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\newcommand{\ptitle}{Photoreceptor activity}
\input{../header.tex}
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
{email: jan.grewe@uni-tuebingen.de}

\begin{document}

\input{../instructions.tex}


%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
\section*{Light responses of an insect photoreceptor.}
In this project you will analyse data from intracellular recordings of
a fly R\,1--6 photoreceptor. These cells show graded membrane
potential changes in response to a light stimulus. The membrane
potential of the photoreceptor was recorded while the cell was
stimulated with a light stimulus. Intracellular recordings often
suffer from drifts in the resting potential. This leads to a large
variability in the responses which is technical and not a cellular
property. To compensate for such drifts trials are aligned to the
resting potential before stimulus onset.

\begin{questions}
  \question{} The accompanying dataset (photoreceptor\_data.zip)
  contains seven mat files. Each of these holds the data from one
  stimulus intensity. In each file are three variables.  (i)
  \textit{voltage} a matrix with the recorded membrane potential from
  10 consecutive trials, (ii) \textit{time} a matrix with the
  time-axis for each trial, and (iii) \textit{trace\_meta} a structure
  that stores several metadata including the \emph{amplitude} value
  that is the voltage used to drive the light stimulus. (Note that
  this voltage is only a proxy for the true light intensity. Twice the
  voltage does not lead to twice the light intensity. Within this
  project, however, you can treat it as if it was the intensity.)

  \begin{parts}
    \part Create a plot of the raw data. For each light intensity plot
    the average response as a function of time. This plot should also
    depict the across-trial variability in an appropriate way.

    \part You will notice that the responses have three main parts, a
    pre-stimulus phase, the phase in which the light was on, and
    finally a post-stimulus phase. Create an characteristic curve that
    plots the response strength as a function of the stimulus
    intensity for the ``onset'' and the ``steady state''
    phases of the light response.

    \part The light switches on at time zero. Estimate the delay
    between stimulus and response.

    \part Analyze the across trial variability in the ``onset'' and
    ``steady state''. Check for statistically significant differences.

    \part The membrane potential shows some fluctuations (noise)
    compare the noise before stimulus onset and in the steady state
    phase of the response.

    \part (optional) You may also analyze the post-stimulus response
    in some more detail.
  \end{parts}
\end{questions}

\end{document}
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