add (bad) method model part
This commit is contained in:
a.ott
parent
59db947745
commit
a9fe4b4149
@ -22,14 +22,23 @@
|
||||
\@writefile{lot}{\select@language{english}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {1}Abstract}{2}{section.1}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {2}Introduction}{2}{section.2}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {3}Materials and Methods}{2}{section.3}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Notes:}{2}{subsection.3.1}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Henriettes structure:}{3}{subsection.3.2}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {4}Results}{4}{section.4}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {5}Discussion}{4}{section.5}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {6}Possible Sources}{4}{section.6}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {6.1}Henriette Walz - Thesis}{4}{subsection.6.1}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.1}Nervous system - Signal encoding}{4}{subsubsection.6.1.1}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.2}electrosensory system - electric fish}{5}{subsubsection.6.1.2}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.3}P-Units encoding}{6}{subsubsection.6.1.3}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.4}Chapter 4 - other models}{6}{subsubsection.6.1.4}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {3}Materials and Methods}{3}{section.3}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Notes:}{3}{subsection.3.1}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Leaky Integrate and Fire Model}{3}{subsection.3.2}}
|
||||
\newlabel{basic_voltage_dynamics}{{1}{4}{Leaky Integrate and Fire Model}{equation.3.1}{}}
|
||||
\newlabel{currents_lifac}{{2}{4}{Leaky Integrate and Fire Model}{equation.3.2}{}}
|
||||
\newlabel{Adaption_dynamics}{{3}{4}{Leaky Integrate and Fire Model}{equation.3.3}{}}
|
||||
\newlabel{full_voltage_dynamics}{{4}{4}{Leaky Integrate and Fire Model}{equation.3.4}{}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Data Generation}{4}{subsection.3.3}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.4}Stimulus Protocols}{4}{subsection.3.4}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.5}Fitting of the Model}{4}{subsection.3.5}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {3.6}Henriette's structure:}{4}{subsection.3.6}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {4}Results}{5}{section.4}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {5}Discussion}{5}{section.5}}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {6}Possible Sources}{5}{section.6}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {6.1}Henriette Walz - Thesis}{5}{subsection.6.1}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.1}Nervous system - Signal encoding}{5}{subsubsection.6.1.1}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.2}electrosensory system - electric fish}{6}{subsubsection.6.1.2}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.3}P-Units encoding}{7}{subsubsection.6.1.3}}
|
||||
\@writefile{toc}{\contentsline {subsubsection}{\numberline {6.1.4}Chapter 4 - other models}{8}{subsubsection.6.1.4}}
|
||||
\@writefile{toc}{\contentsline {subsection}{\numberline {6.2}Zakon: Negative Interspike Interval Correlations Increase the Neuronal Capacity for Encoding Time-Dependent Stimuli}{8}{subsection.6.2}}
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex 2018.11.12) 6 JUL 2020 16:24
|
||||
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex 2018.11.12) 14 JUL 2020 15:39
|
||||
entering extended mode
|
||||
restricted \write18 enabled.
|
||||
%&-line parsing enabled.
|
||||
@ -373,20 +373,20 @@ Package: listings 2015/06/04 1.6 (Carsten Heinz)
|
||||
(./Masterthesis.aux)
|
||||
\openout1 = `Masterthesis.aux'.
|
||||
|
||||
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 20.
|
||||
LaTeX Font Info: ... okay on input line 20.
|
||||
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 24.
|
||||
LaTeX Font Info: ... okay on input line 24.
|
||||
|
||||
*geometry* detected driver: pdftex
|
||||
*geometry* verbose mode - [ preamble ] result:
|
||||
@ -450,7 +450,7 @@ File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv
|
||||
e
|
||||
))
|
||||
\AtBeginShipoutBox=\box34
|
||||
Package hyperref Info: Link coloring OFF on input line 20.
|
||||
Package hyperref Info: Link coloring OFF on input line 24.
|
||||
|
||||
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
|
||||
Package: nameref 2012/10/27 v2.43 Cross-referencing by name of section
|
||||
@ -460,9 +460,9 @@ Package: gettitlestring 2010/12/03 v1.4 Cleanup title references (HO)
|
||||
)
|
||||
\c@section@level=\count137
|
||||
)
|
||||
LaTeX Info: Redefining \ref on input line 20.
|
||||
LaTeX Info: Redefining \pageref on input line 20.
|
||||
LaTeX Info: Redefining \nameref on input line 20.
|
||||
LaTeX Info: Redefining \ref on input line 24.
|
||||
LaTeX Info: Redefining \pageref on input line 24.
|
||||
LaTeX Info: Redefining \nameref on input line 24.
|
||||
|
||||
(./Masterthesis.out) (./Masterthesis.out)
|
||||
\@outlinefile=\write3
|
||||
@ -494,7 +494,7 @@ ination with the same identifier (name{page.1}) has been already used, duplicat
|
||||
e ignored
|
||||
<to be read again>
|
||||
\relax
|
||||
l.69 \newpage
|
||||
l.73 \newpage
|
||||
\newpage [1] (./Masterthesis.toc)
|
||||
\tf@toc=\write4
|
||||
\openout4 = `Masterthesis.toc'.
|
||||
@ -502,39 +502,50 @@ l.69 \newpage
|
||||
[2] [3]
|
||||
(/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-32.def
|
||||
File: uni-32.def 2013/05/13 UCS: Unicode data U+2000..U+20FF
|
||||
) [4] [5]
|
||||
) [4] [5] [6]
|
||||
(/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-34.def
|
||||
File: uni-34.def 2013/05/13 UCS: Unicode data U+2200..U+22FF
|
||||
) [6]
|
||||
Package atveryend Info: Empty hook `BeforeClearDocument' on input line 316.
|
||||
[7]
|
||||
Package atveryend Info: Empty hook `AfterLastShipout' on input line 316.
|
||||
) [7]
|
||||
Package atveryend Info: Empty hook `BeforeClearDocument' on input line 383.
|
||||
[8]
|
||||
Package atveryend Info: Empty hook `AfterLastShipout' on input line 383.
|
||||
|
||||
(./Masterthesis.aux)
|
||||
Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 316.
|
||||
Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 316.
|
||||
Package rerunfilecheck Info: File `Masterthesis.out' has not changed.
|
||||
(rerunfilecheck) Checksum: 0B9FD88A560E631C1F998F25D3006481;817.
|
||||
Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 316.
|
||||
Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 383.
|
||||
Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 383.
|
||||
|
||||
|
||||
Package rerunfilecheck Warning: File `Masterthesis.out' has changed.
|
||||
(rerunfilecheck) Rerun to get outlines right
|
||||
(rerunfilecheck) or use package `bookmark'.
|
||||
|
||||
Package rerunfilecheck Info: Checksums for `Masterthesis.out':
|
||||
(rerunfilecheck) Before: E5A01AD1DD40BB8E82354B986D49E92E;1097
|
||||
(rerunfilecheck) After: B518E8D1F778500C8E13AC0FC596ED6A;1261.
|
||||
Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 383.
|
||||
)
|
||||
Here is how much of TeX's memory you used:
|
||||
11015 strings out of 493029
|
||||
155976 string characters out of 6136233
|
||||
259481 words of memory out of 5000000
|
||||
14342 multiletter control sequences out of 15000+600000
|
||||
8867 words of font info for 32 fonts, out of 8000000 for 9000
|
||||
11043 strings out of 493029
|
||||
156320 string characters out of 6136233
|
||||
259783 words of memory out of 5000000
|
||||
14355 multiletter control sequences out of 15000+600000
|
||||
9214 words of font info for 33 fonts, out of 8000000 for 9000
|
||||
1141 hyphenation exceptions out of 8191
|
||||
37i,11n,38p,417b,561s stack positions out of 5000i,500n,10000p,200000b,80000s
|
||||
37i,11n,38p,618b,561s stack positions out of 5000i,500n,10000p,200000b,80000s
|
||||
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></us
|
||||
r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share
|
||||
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/share/texliv
|
||||
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-
|
||||
dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f
|
||||
onts/type1/public/amsfonts/cm/cmsy8.pfb>
|
||||
Output written on Masterthesis.pdf (8 pages, 86985 bytes).
|
||||
r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/shar
|
||||
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texl
|
||||
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/tex
|
||||
mf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist
|
||||
/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/
|
||||
type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
|
||||
blic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
|
||||
msfonts/cm/cmsy8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts
|
||||
/cm/cmti12.pfb>
|
||||
Output written on Masterthesis.pdf (9 pages, 131291 bytes).
|
||||
PDF statistics:
|
||||
231 PDF objects out of 1000 (max. 8388607)
|
||||
212 compressed objects within 3 object streams
|
||||
98 named destinations out of 1000 (max. 500000)
|
||||
105 words of extra memory for PDF output out of 10000 (max. 10000000)
|
||||
286 PDF objects out of 1000 (max. 8388607)
|
||||
262 compressed objects within 3 object streams
|
||||
112 named destinations out of 1000 (max. 500000)
|
||||
137 words of extra memory for PDF output out of 10000 (max. 10000000)
|
||||
|
||||
|
||||
@ -2,12 +2,17 @@
|
||||
\BOOKMARK [1][]{section.2}{Introduction}{}% 2
|
||||
\BOOKMARK [1][]{section.3}{Materials and Methods}{}% 3
|
||||
\BOOKMARK [2][]{subsection.3.1}{Notes:}{section.3}% 4
|
||||
\BOOKMARK [2][]{subsection.3.2}{Henriettes structure:}{section.3}% 5
|
||||
\BOOKMARK [1][]{section.4}{Results}{}% 6
|
||||
\BOOKMARK [1][]{section.5}{Discussion}{}% 7
|
||||
\BOOKMARK [1][]{section.6}{Possible Sources}{}% 8
|
||||
\BOOKMARK [2][]{subsection.6.1}{Henriette Walz - Thesis}{section.6}% 9
|
||||
\BOOKMARK [3][]{subsubsection.6.1.1}{Nervous system - Signal encoding}{subsection.6.1}% 10
|
||||
\BOOKMARK [3][]{subsubsection.6.1.2}{electrosensory system - electric fish}{subsection.6.1}% 11
|
||||
\BOOKMARK [3][]{subsubsection.6.1.3}{P-Units encoding}{subsection.6.1}% 12
|
||||
\BOOKMARK [3][]{subsubsection.6.1.4}{Chapter 4 - other models}{subsection.6.1}% 13
|
||||
\BOOKMARK [2][]{subsection.3.2}{Leaky Integrate and Fire Model}{section.3}% 5
|
||||
\BOOKMARK [2][]{subsection.3.3}{Data Generation}{section.3}% 6
|
||||
\BOOKMARK [2][]{subsection.3.4}{Stimulus Protocols}{section.3}% 7
|
||||
\BOOKMARK [2][]{subsection.3.5}{Fitting of the Model}{section.3}% 8
|
||||
\BOOKMARK [2][]{subsection.3.6}{Henriette's structure:}{section.3}% 9
|
||||
\BOOKMARK [1][]{section.4}{Results}{}% 10
|
||||
\BOOKMARK [1][]{section.5}{Discussion}{}% 11
|
||||
\BOOKMARK [1][]{section.6}{Possible Sources}{}% 12
|
||||
\BOOKMARK [2][]{subsection.6.1}{Henriette Walz - Thesis}{section.6}% 13
|
||||
\BOOKMARK [3][]{subsubsection.6.1.1}{Nervous system - Signal encoding}{subsection.6.1}% 14
|
||||
\BOOKMARK [3][]{subsubsection.6.1.2}{electrosensory system - electric fish}{subsection.6.1}% 15
|
||||
\BOOKMARK [3][]{subsubsection.6.1.3}{P-Units encoding}{subsection.6.1}% 16
|
||||
\BOOKMARK [3][]{subsubsection.6.1.4}{Chapter 4 - other models}{subsection.6.1}% 17
|
||||
\BOOKMARK [2][]{subsection.6.2}{Zakon: Negative Interspike Interval Correlations Increase the Neuronal Capacity for Encoding Time-Dependent Stimuli}{section.6}% 18
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -14,6 +14,10 @@
|
||||
|
||||
|
||||
|
||||
\newcommand{\todo}[1]{{(\color{red} TODO: #1) }}
|
||||
\newcommand{\AptLepto}{{\textit{Apteronotus leptorhynchus}}}
|
||||
\newcommand{\lepto}{{\textit{A. leptorhynchus}}}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Ab hier beginnt der eigentliche Text:
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
@ -109,7 +113,7 @@ Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in
|
||||
\item p-type neurons code AMs
|
||||
\end{enumerate}
|
||||
|
||||
\item goal be able to simulate heterogenic population to analyse full coding properties -> many cells at the same time needed -> only possible in vitro/ with model simulations
|
||||
\item goal be able to simulate heterogenic population to analyze full coding properties -> many cells at the same time needed -> only possible in vitro/ with model simulations
|
||||
|
||||
\item Possible to draw representative values for model parameters to generate a population ?
|
||||
|
||||
@ -128,8 +132,9 @@ Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in
|
||||
\begin{enumerate}
|
||||
\item How data was measured / which data used
|
||||
\item How data was chosen -> at least 30s baseline, 7 contrasts with 7 trials
|
||||
\item experimental protocells were allowed by XYZ (before 2012: All experimental protocols were approved and complied with national and regional laws (file no. 55.2-1-54-2531-135-09). between 2013-2016 ZP 1/13 Regierungspräsidium Tübingen and after 2016 ZP 1/16 Regierungspräsidium Tübingen)
|
||||
\item experimental protocols were allowed by XYZ (before 2012: All experimental protocols were approved and complied with national and regional laws (file no. 55.2-1-54-2531-135-09). between 2013-2016 ZP 1/13 Regierungspräsidium Tübingen and after 2016 ZP 1/16 Regierungspräsidium Tübingen)
|
||||
\item description of data -> Baseline properties, FI-Curve with images made from cells
|
||||
\item make a point of using also bursty cells as part of what is new in this work!
|
||||
\end{enumerate}
|
||||
|
||||
\item behavior parameters:
|
||||
@ -145,10 +150,10 @@ Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in
|
||||
\item parameters explanation, dif. equations
|
||||
\item Explain addition of adaption current
|
||||
\item note addition of noise + factor for the independence from step size
|
||||
\item addition of refractory period
|
||||
\item check between alpha in fire-rate model adaption and a-delta in LIFAC
|
||||
\end{enumerate}
|
||||
|
||||
|
||||
\item Fitting of model to data
|
||||
\begin{enumerate}
|
||||
\item which variables where determined beforehand (None, just for start parameters)
|
||||
@ -159,14 +164,78 @@ Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in
|
||||
\end{enumerate}
|
||||
|
||||
|
||||
\subsection{Henriettes structure:}
|
||||
\subsection{Leaky Integrate and Fire Model}
|
||||
|
||||
% add info about simulation by euler integration and which time steps!
|
||||
% show voltage dynamics with resistance :
|
||||
also show function with membrane resistance before explaining that is is unknown an left out: $ \tau_m \frac{dV}{dt} = -V + I$
|
||||
% explain subthreshold behaviour first then add V_{th} and adaption etc
|
||||
% explain modeling of the adaption current see Benda2010
|
||||
% table with explanation of variables ?
|
||||
\todo{restructure sounds horrible}
|
||||
|
||||
The P-units were modeled with an noisy leaky integrate-and-fire neuron with an adaption current (LIFAC). The basic voltage dynamics in this model follows equation \ref{basic_voltage_dynamics}. The voltage is integrated over time while also exponentially decaying back to zero. When a voltage threshold is reached the voltage is set back to zero and a spike is recorded. The currents in this model carry the unit mV as the the cell bodies of p-units are inaccessible during the recordings and as such the resistance of the cell membrane is unknown \todo{ref mem res p-units}.
|
||||
|
||||
The current can be split into three parts: the adaption current, the input current and the bias current (Eq. \ref{currents_lifac}). The input current is the stimulus from outside the cell, the bias current models the general activity of the cell and the adaption current models a combination of the M-type, mAHP-type and sodium adaption currents \todo{ref Benda 2005}.
|
||||
|
||||
The adaption current is modeled as an exponential decay with the time constant $\tau_A$ and a strength called $\Delta_A$ (Eq. \ref{Adaption_dynamics}). $\Delta_A$ is multiplied with the sum of events in the spike train ($\delta (t)$) of the model cell itself. For the simulation using the Euler integration this results in an increase of $I_A$ by $\Delta_A$ in every time step where a spike is recorded. \todo{image of model simulation with voltage adaption and spikes?}
|
||||
|
||||
Finally a noise current and an absolute refractory period where added to the model. The noise $\xi$ is drawn in from a Gaussian noise with values between 0 and 1 and divided by $\sqrt{\Delta t}$ to get a noise which autocorrelation function is independent of the integration step size $\Delta t$. After an excitation of the model the voltage is kept at zero for the duration of the refractory period.
|
||||
|
||||
|
||||
\begin{equation}
|
||||
\tau_m \frac{dV}{dt} = -V + I
|
||||
\label{basic_voltage_dynamics}
|
||||
\end{equation}
|
||||
|
||||
\begin{equation}
|
||||
I = \alpha I_{Input} - I_A + I_{Bias}
|
||||
\label{currents_lifac}
|
||||
\end{equation}
|
||||
|
||||
\begin{equation}
|
||||
\tau_A \frac{dI_A}{dt} = -I_A + \Delta_A \sum \delta (t)
|
||||
\label{Adaption_dynamics}
|
||||
\end{equation}
|
||||
|
||||
\begin{equation}
|
||||
\tau_m \frac{dV}{dt} = -V+I_{Bias} +\alpha I_{Input} - I_{A} + \sqrt{2D}\frac{\xi}{\sqrt{\Delta t}}
|
||||
\label{full_voltage_dynamics}
|
||||
\end{equation}
|
||||
|
||||
|
||||
|
||||
\subsection{Data Generation}
|
||||
|
||||
The data for this master's thesis was collected as part of other previous studies \todo{ref other studies}. The collection method provided here is only an overview for the exact details see \todo{link papers}.
|
||||
The in vivo intracellular recordings of P-unit electroreceptors of \AptLepto were done in the lateral line nerve . The fish were an anesthetized with MS-222 (100-130 mg/l; PharmaQ; Fordingbridge, UK) and the part of the skin covering the lateral line just behind the skull was removed
|
||||
|
||||
|
||||
general anesthetic MS-222 (100-130 mg/l; PharmaQ; Fordingbridge, UK)
|
||||
local anesthetics Lidocaine (2\%; bela-pharm; Vechta, Germany)
|
||||
immobilization with (Tubocurarine; Sigma-Aldrich; Steinheim, Germany, 25–50 $\mu l$ of 5\. mg/ml solution)
|
||||
|
||||
|
||||
\subsection{Stimulus Protocols}
|
||||
% image of Baseline stimulus as baseline doesn't mean no stimulus here
|
||||
% image of Fi curve stimulus sinusoidal step
|
||||
% image of SAM stimulus
|
||||
|
||||
|
||||
\subsection{Fitting of the Model}
|
||||
|
||||
|
||||
|
||||
|
||||
\subsection{Henriette's structure:}
|
||||
|
||||
\begin{enumerate}
|
||||
|
||||
\item data generation - recordings
|
||||
\item model simulations - construction of model
|
||||
\item Simulation protocols
|
||||
\item Data analysis - calculation of behaviour parameters \begin{enumerate}
|
||||
\item Data analysis - calculation of behavior parameters
|
||||
\begin{enumerate}
|
||||
\item calculation of baseline parameters
|
||||
\item calculation of fi curve parameters
|
||||
\item stimuli step SAM(?) noise(?)
|
||||
@ -210,16 +279,14 @@ Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in
|
||||
\item encoding info in inter spike intervals (Singer and Gary 1995)
|
||||
\item encoding time window (Theunissen and Miller 1995) "This time window is the time scale in which the encoding is assumed to take placewithin the nervous system
|
||||
\item encoding is noisy (Mainen and Sejnowski 1995, Tolhurst et al 1983, Tomko and Crapper 1974 -> review Faisal et al 2008) in part because of stimulus properties but also cell properties (Ion channel stochasticity (van Rossum et al.,2003))
|
||||
\item noise can be beneficial to encoding -> “stochastic
|
||||
resonance” (weak stimuli on thresholding devices like neurons, noice allows coding of sub threshold stimuli) (Benzi et al., 1981)
|
||||
\item single neurons are anatomically and computationally independant units, the
|
||||
\item noise can be beneficial to encoding -> "stochastic resonance" (weak stimuli on thresholding devices like neurons, noise allows coding of sub threshold stimuli) (Benzi et al., 1981)
|
||||
\item single neurons are anatomically and computationally independent units, the
|
||||
representation and processing of information in vertebrate nervous systems is distributed
|
||||
over groups or networks of cells (for a review, see Pouget et al., 2000)
|
||||
\item It has
|
||||
been shown that the synchrony among cells carries information on a very fine temporal
|
||||
scale in different modalities, from olfaction (Laurent, 1996) to vision (Dan et al., 1998)
|
||||
\item In the electrosensory system it was shown before that communica-
|
||||
tion signals change the synchrony of the receptor population (Benda et al., 2005, 2006)
|
||||
\item In the electrosensory system it was shown before that communication signals change the synchrony of the receptor population (Benda et al., 2005, 2006)
|
||||
and that this is read out by cells in the successive stages of the electrosensory pathway
|
||||
(Marsat and Maler, 2010, 2012; Marsat et al., 2009).
|
||||
\item An advantage of rate coding in populations is that it is fast. The rate in
|
||||
@ -232,33 +299,26 @@ even if the stimulus is strong enough to trigger action potentials itself (supra
|
||||
stochastic resonance described by Stocks, 2000; see Fig. 1.1 B
|
||||
\item Cells of the same type and from the same population often vary in their stimulus sen-
|
||||
sitivity (Ringach et al., 2002) as well as in their baseline activity properties (Gussin et al., 2007; Hospedales et al., 2008)
|
||||
\item Heterogeneity has been shown to improve infor-
|
||||
mation coding in both situations, in the presence of noise correlations, for example in
|
||||
\item Heterogeneity has been shown to improve information coding in both situations, in the presence of noise correlations, for example in
|
||||
the visual system cells (Chelaru and Dragoi, 2008) or when correlations mainly originate
|
||||
from shared input as in the olfactory system (Padmanabhan and Urban, 2010)
|
||||
\item A prerequisite to a neural code thus is that it can be read out by other neurons (Perkel
|
||||
and Bullock, 1968).
|
||||
\item Developement and evolution shape the func-
|
||||
tioning of many physiological systems and there is evidence that they also shape the
|
||||
encoding mechanisms of nervous systems. For example, the development of frequency
|
||||
\item Development and evolution shape the functioning of many physiological systems and there is evidence that they also shape the encoding mechanisms of nervous systems. For example, the development of frequency
|
||||
selectivity in the auditory cortex has been shown to be delayed in animals stimulated
|
||||
with white noise only (Chang and Merzenich, 2003). Also, several encoding mecha-
|
||||
nisms can be related to the selective pressure that the energetic consumption of the ner-
|
||||
vous system has exerted on its evolution (Laughlin, 2001; Niven and Laughlin, 2008).
|
||||
with white noise only (Chang and Merzenich, 2003). Also, several encoding mechanisms can be related to the selective pressure that the energetic consumption of the nervous system has exerted on its evolution (Laughlin, 2001; Niven and Laughlin, 2008).
|
||||
These finding conformed earlier theoretical predictions that had proposed that coding
|
||||
should be optimised to encode natural stimuli in an energy-efficient way (Barlow, 1972). -> importance of using natrual stimuli as the coding and nervous system could be optimised for unknown stimuli features not contained in the artificial stimuli like white noise.
|
||||
should be optimized to encode natural stimuli in an energy-efficient way (Barlow, 1972). -> importance of using natural stimuli as the coding and nervous system could be optimized for unknown stimuli features not contained in the artificial stimuli like white noise.
|
||||
\end{enumerate}
|
||||
\subsubsection{electrosensory system - electric fish}
|
||||
|
||||
\begin{enumerate}
|
||||
\item For decades, studies examining the neurophysiological systems of weakly electric
|
||||
fish have provided insights into how natural behaviours are generated using relatively
|
||||
fish have provided insights into how natural behaviors are generated using relatively
|
||||
simple sensorimotor circuits (for recent reviews see: Chacron et al., 2011; Fortune, 2006;
|
||||
Marsat and Maler, 2012). Further, electrocommunication signals are relatively easy to
|
||||
describe, classify and simulate, facilitating quantification and experimental manipula-
|
||||
tion. Weakly electric fish are therefore an ideal system for examining how communica-
|
||||
tion signals influence sensory scenes, drive sensory system responses, and consequently
|
||||
exert effects on conspecific behaviour.
|
||||
describe, classify and simulate, facilitating quantification and experimental manipulation. Weakly electric fish are therefore an ideal system for examining how communication signals influence sensory scenes, drive sensory system responses, and consequently
|
||||
exert effects on conspecific behavior.
|
||||
\item The weakly electric fish use active electroreception to navigate and communicate under
|
||||
low light conditions (Zupanc et al., 2001).
|
||||
\item In active electroreception, animals produce
|
||||
@ -267,8 +327,8 @@ electric organ discharge, EOD) and infer, from changes of the EOD, information a
|
||||
the location and identification of objects and conspecifics in their vicinity (e.g. Kelly
|
||||
et al., 2008; MacIver et al., 2001). However, perturbations result not only from objects
|
||||
and other fish, but also from self-motion and other factors. All of these together make
|
||||
up the electrosensory scene. The perturbed version of the fish’s own field on its skin
|
||||
is called the electric image (Caputi and Budelli, 2006), which is sensed via specialised
|
||||
up the electrosensory scene. The perturbed version of the fish's own field on its skin
|
||||
is called the electric image (Caputi and Budelli, 2006), which is sensed via specialized
|
||||
receptors distributed over the body surface (Carr et al., 1982).
|
||||
\item In A. leptorhynchus, the
|
||||
dipole-like electric field (electric organ discharge, EOD) oscillates in a quasi-sinusoidal
|
||||
@ -279,8 +339,7 @@ has a specific frequency (the EOD frequency, EODf) that remains stable in time (
|
||||
ing a coefficient of variation of the interspikes intervals as low as $2 ∗ 10^{−4} $; Moortgat et al., 1998).
|
||||
\item During social encounters, wave-type fish often modulate the frequency as
|
||||
well as the amplitude of their field to communicate (Hagedorn and Heiligenberg, 1985).
|
||||
\item Communication signals in A. leptorhynchus have been clas-
|
||||
sified into two classes: (i) chirps are transient and stereotyped EODf excursions over
|
||||
\item Communication signals in A. leptorhynchus have been classified into two classes: (i) chirps are transient and stereotyped EODf excursions over
|
||||
tens of milliseconds (Zupanc et al., 2006), while (ii) rises are longer duration and more
|
||||
variable modulations of EODf, typically lasting for hundreds of milliseconds to sec-
|
||||
onds (Hagedorn and Heiligenberg, 1985; Tallarovic and Zakon, 2002). (OLD INFO ? RISES NOW OVER MINUTES/HOURS)
|
||||
@ -314,4 +373,11 @@ dynamical threshold.
|
||||
tation current to reproduce the high-pass behaviour of P-units.
|
||||
\end{enumerate}
|
||||
|
||||
|
||||
\subsection{Zakon: Negative Interspike Interval Correlations Increase the Neuronal
|
||||
Capacity for Encoding Time-Dependent Stimuli}
|
||||
|
||||
\begin{enumerate}
|
||||
\item P-type electroreceptors on their skin detect amplitude modulations (AMs) of this field caused by nearby objects or conspecifics (for review, see Bastian, 1981; Zakon, 1986).
|
||||
\end{enumerate}
|
||||
\end{document}
|
||||
@ -1,14 +1,19 @@
|
||||
\select@language {english}
|
||||
\contentsline {section}{\numberline {1}Abstract}{2}{section.1}
|
||||
\contentsline {section}{\numberline {2}Introduction}{2}{section.2}
|
||||
\contentsline {section}{\numberline {3}Materials and Methods}{2}{section.3}
|
||||
\contentsline {subsection}{\numberline {3.1}Notes:}{2}{subsection.3.1}
|
||||
\contentsline {subsection}{\numberline {3.2}Henriettes structure:}{3}{subsection.3.2}
|
||||
\contentsline {section}{\numberline {4}Results}{4}{section.4}
|
||||
\contentsline {section}{\numberline {5}Discussion}{4}{section.5}
|
||||
\contentsline {section}{\numberline {6}Possible Sources}{4}{section.6}
|
||||
\contentsline {subsection}{\numberline {6.1}Henriette Walz - Thesis}{4}{subsection.6.1}
|
||||
\contentsline {subsubsection}{\numberline {6.1.1}Nervous system - Signal encoding}{4}{subsubsection.6.1.1}
|
||||
\contentsline {subsubsection}{\numberline {6.1.2}electrosensory system - electric fish}{5}{subsubsection.6.1.2}
|
||||
\contentsline {subsubsection}{\numberline {6.1.3}P-Units encoding}{6}{subsubsection.6.1.3}
|
||||
\contentsline {subsubsection}{\numberline {6.1.4}Chapter 4 - other models}{6}{subsubsection.6.1.4}
|
||||
\contentsline {section}{\numberline {3}Materials and Methods}{3}{section.3}
|
||||
\contentsline {subsection}{\numberline {3.1}Notes:}{3}{subsection.3.1}
|
||||
\contentsline {subsection}{\numberline {3.2}Leaky Integrate and Fire Model}{3}{subsection.3.2}
|
||||
\contentsline {subsection}{\numberline {3.3}Data Generation}{4}{subsection.3.3}
|
||||
\contentsline {subsection}{\numberline {3.4}Stimulus Protocols}{4}{subsection.3.4}
|
||||
\contentsline {subsection}{\numberline {3.5}Fitting of the Model}{4}{subsection.3.5}
|
||||
\contentsline {subsection}{\numberline {3.6}Henriette's structure:}{4}{subsection.3.6}
|
||||
\contentsline {section}{\numberline {4}Results}{5}{section.4}
|
||||
\contentsline {section}{\numberline {5}Discussion}{5}{section.5}
|
||||
\contentsline {section}{\numberline {6}Possible Sources}{5}{section.6}
|
||||
\contentsline {subsection}{\numberline {6.1}Henriette Walz - Thesis}{5}{subsection.6.1}
|
||||
\contentsline {subsubsection}{\numberline {6.1.1}Nervous system - Signal encoding}{5}{subsubsection.6.1.1}
|
||||
\contentsline {subsubsection}{\numberline {6.1.2}electrosensory system - electric fish}{6}{subsubsection.6.1.2}
|
||||
\contentsline {subsubsection}{\numberline {6.1.3}P-Units encoding}{7}{subsubsection.6.1.3}
|
||||
\contentsline {subsubsection}{\numberline {6.1.4}Chapter 4 - other models}{8}{subsubsection.6.1.4}
|
||||
\contentsline {subsection}{\numberline {6.2}Zakon: Negative Interspike Interval Correlations Increase the Neuronal Capacity for Encoding Time-Dependent Stimuli}{8}{subsection.6.2}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user