introduction base of population coding

thesis/Masterthesis.bbl

@@ -17,6 +17,11 @@ Benda, J., Maler, L., and Longtin, A. (2010).
   adaptation currents or dynamic thresholds.
 \newblock {\em Journal of Neurophysiology}, 104(5):2806--2820.
 
+\bibitem[Chacron et~al., 2001]{chacron2001simple}
+Chacron, M.~J., Longtin, A., and Maler, L. (2001).
+\newblock Simple models of bursting and non-bursting p-type electroreceptors.
+\newblock {\em Neurocomputing}, 38:129--139.
+
 \bibitem[Gao and Han, 2012]{gao2012implementing}
 Gao, F. and Han, L. (2012).
 \newblock Implementing the nelder-mead simplex algorithm with adaptive
@@ -29,6 +34,11 @@ Gussin, D., Benda, J., and Maler, L. (2007).
   afferents.
 \newblock {\em Journal of neurophysiology}, 97(4):2917--2929.
 
+\bibitem[Kashimori et~al., 1996]{kashimori1996model}
+Kashimori, Y., Goto, M., and Kambara, T. (1996).
+\newblock Model of p-and t-electroreceptors of weakly electric fish.
+\newblock {\em Biophysical journal}, 70(6):2513--2526.
+
 \bibitem[Maciver et~al., 2001]{maciver2001prey}
 Maciver, M.~A., Sharabash, N.~M., and Nelson, M.~E. (2001).
 \newblock Prey-capture behavior in gymnotid electric fish: motion analysis and

thesis/Masterthesis.blg

@@ -1,46 +1,46 @@
-This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
-Capacity: max_strings=35307, hash_size=35307, hash_prime=30011
+This is BibTeX, Version 0.99d (TeX Live 2017/Debian)
+Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
 The top-level auxiliary file: Masterthesis.aux
 The style file: apalike.bst
 Database file #1: citations.bib
-You've used 11 entries,
+You've used 13 entries,
             1935 wiz_defined-function locations,
-            552 strings with 5925 characters,
-and the built_in function-call counts, 4542 in all, are:
-= -- 453
-> -- 182
+            566 strings with 6261 characters,
+and the built_in function-call counts, 5413 in all, are:
+= -- 541
+> -- 218
 < -- 3
-+ -- 62
-- -- 60
-* -- 423
-:= -- 793
-add.period$ -- 33
-call.type$ -- 11
-change.case$ -- 84
-chr.to.int$ -- 11
-cite$ -- 11
-duplicate$ -- 152
-empty$ -- 318
-format.name$ -- 75
-if$ -- 866
++ -- 74
+- -- 72
+* -- 504
+:= -- 943
+add.period$ -- 39
+call.type$ -- 13
+change.case$ -- 100
+chr.to.int$ -- 13
+cite$ -- 13
+duplicate$ -- 180
+empty$ -- 379
+format.name$ -- 89
+if$ -- 1033
 int.to.chr$ -- 1
 int.to.str$ -- 0
-missing$ -- 10
-newline$ -- 58
-num.names$ -- 33
-pop$ -- 61
+missing$ -- 12
+newline$ -- 68
+num.names$ -- 39
+pop$ -- 73
 preamble$ -- 1
-purify$ -- 85
+purify$ -- 101
 quote$ -- 0
-skip$ -- 113
+skip$ -- 133
 stack$ -- 0
-substring$ -- 380
-swap$ -- 11
+substring$ -- 460
+swap$ -- 13
 text.length$ -- 0
 text.prefix$ -- 0
 top$ -- 0
-type$ -- 66
+type$ -- 78
 warning$ -- 0
-while$ -- 41
+while$ -- 49
 width$ -- 0
-write$ -- 145
+write$ -- 171

thesis/Masterthesis.tex

@@ -142,7 +142,8 @@ Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in
 
 The environment of an organism holds important information that it needs to survive. Information about predators to avoid, food to find and potential mates. That means that the ability to sense and process this information is of vital importance for any organism. At the same time the environment also contains a lot of information that is irrelevant to an organism. \todo{ref} suggested already that the sensory systems of an organism should be specialized to extract the information it needs while filtering out the noise and irrelevant information, to efficiently use the limited coding capacity of the sensory systems.
 
-\todo{path to electric fish}
+One interesting model system for questions of perception and signal encoding is the electric fish \AptLepto
+\todo{path to electric fish: good as a model system with electric sense}
 
 The electric fish \AptLepto (Brown ghost knife fish) generate a sinusoidal electric field with the electric organ in their tail enabling them to use active electroreception which they use to find prey and communicate with each other (\cite{maciver2001prey}, \cite{zupanc2006electric}). The different use cases of this electric organ discharge (EOD) come with the necessity to detect a wide range of different amplitude modulations (AMs). Electrolocation of object in the surrounding water like small prey or rocks cause small low frequency AMs \citep{babineau2007spatial}. At the same time other electric fish can cause stronger and higher frequency AMs through interference between the electric fields and their communication signals like chirps, short increases in their EOD frequency \citep{zupanc2006electric}. This means that the electroreceptors need to be able to encode a wide range of changes in EOD amplitude, in speed as well as strength.
 The EOD and its AMs are encoded by electroreceptor organs in the skin. \lepto have two kinds of tuberous electrosensory organs: the T and P type units \citep{scheich1973coding}. The T units (time coder) are strongly phase locked to the EOD and fire regularly once every EOD period. They encode the phase of the EOD in their spike timing. The P units (probability coders) on the other hand do not fire every EOD period. Instead they fire irregularly with a certain probability that depends on the EOD amplitude. That way they encode information about the EOD amplitude in their firing probability \citep{scheich1973coding}. An example of the firing behavior of a P unit is shown in figure~\ref{fig:p_unit_example}. 
@@ -164,10 +165,15 @@ When the fish's EOD is unperturbed P units fire every few EOD periods but they h
 {\includegraphics[width=1\textwidth]{figures/isi_hist_heterogeneity.png}}
 \end{figure}
 
-\todo{heterogeneity}
+\todo{heterogeneity more}
+
+Furthermore show P units a pronounced heterogeneity in their spiking behavior (fig.~\ref{fig:heterogeneity_isi_hist}, \cite{gussin2007limits}). This is an important aspect one needs to consider when trying to understand what and how information is encoded in the spike trains of the neuron. A single neuron might be an independent unit from all other neurons but through different tuning curves a full picture of the stimulus can be encoded in the population while a single neuron only encodes a small feature space. This type of encoding is ubiquitous in the nervous system and is used in (EXAMPLE) for (EXAMPLE feature) PLUS MORE... \todo{refs}. Even though P units were already modelled based on a simple leaky integrate-and-fire neuron \citep{chacron2001simple} and conductance based \citep{kashimori1996model} and well studied (\todo{refS}), but up to this point there no model that tries to cover the full breadth of heterogeneity of the P unit population. Having such a model could help shed light into the population code used in the electric sense, allow researchers gain a better picture how higher brain areas might process the information and get one step closer to the full path between sensory input and behavioural output.
+
+
+
+
+
 
-Furthermore show P units a pronounced heterogeneity in their spiking behavior (fig.~\ref{fig:heterogeneity_isi_hist}, \cite{gussin2007limits}). 
-\todo{population coding}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Methoden
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -221,7 +227,7 @@ V_{Stim}(t) = EOD(t)(1 + AM(t))
 
 \begin{figure}[H]
 \floatbox[{\capbeside\thisfloatsetup{capbesideposition={left, center}, capbesidewidth=0.45\textwidth}}]{figure}[\FBwidth]
-{\caption{\label{fig:stim_examples} Example of the stimulus construction. At the top a recording of the fish's EOD. In the middle: EOD recording multiplied with the AM, with a step between 0 and 50\,ms to a contrast of 30\,\% (marked in \todo{color}). At the bottom the resulting stimulus trace when the AM is added to the EOD. \todo{Umformulieren}}}
+{\caption{\label{fig:stim_examples} Example of the stimulus construction. At the top a recording of the fish's EOD. In the middle: EOD recording multiplied with the AM, with a step between 0 and 50\,ms to a contrast of 30\,\% (marked in \todo{color}). At the bottom the resulting stimulus trace when the AM is added to the EOD. \todo{Umformulieren add figure labels A, B, C}}}
 {\includegraphics[width=0.45\textwidth]{figures/amGeneration.pdf}}
 \end{figure}