diff --git a/spike_trains/lecture/Makefile b/spike_trains/lecture/Makefile new file mode 100644 index 0000000..96b7d0e --- /dev/null +++ b/spike_trains/lecture/Makefile @@ -0,0 +1,20 @@ +TEXFILES=$(wildcard *.tex) +TEXFILES=psth_sta.tex + +PDFFILES=$(TEXFILES:.tex=.pdf) + +pdf : $(PDFFILES) + +$(PDFFILES) : %.pdf : %.tex + pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true + +clean : + rm -f *~ $(TEXFILES:.tex=.aux) $(TEXFILES:.tex=.log) $(TEXFILES:.tex=.out) $(TEXFILES:.tex=.nav) $(TEXFILES:.tex=.snm) $(TEXFILES:.tex=.toc) $(TEXFILES:.tex=.vrb) + +cleanall : clean + rm -f $(PDFFILES) + +watch : + while true; do ! make -q pdf && make pdf; sleep 0.5; done + + diff --git a/spike_trains/lecture/beamercolorthemetuebingen.sty b/spike_trains/lecture/beamercolorthemetuebingen.sty new file mode 100644 index 0000000..c4a5da6 --- /dev/null +++ b/spike_trains/lecture/beamercolorthemetuebingen.sty @@ -0,0 +1,61 @@ +% Copyright 2007 by Till Tantau +% +% This file may be distributed and/or modified +% +% 1. under the LaTeX Project Public License and/or +% 2. under the GNU Public License. +% +% See the file doc/licenses/LICENSE for more details. + +\usepackage{color} +\definecolor{karminrot}{RGB}{165,30,55} +\definecolor{gold}{RGB}{180,160,105} +\definecolor{anthrazit}{RGB}{50 ,65 ,75 } + +\mode + +\setbeamercolor*{normal text}{fg=anthrazit,bg=white} +\setbeamercolor*{alerted text}{fg=anthrazit} +\setbeamercolor*{example text}{fg=anthrazit} +\setbeamercolor*{structure}{fg=gold,bg=karminrot} + +\providecommand*{\beamer@bftext@only}{% + \relax + \ifmmode + \expandafter\beamer@bftext@warning + \else + \expandafter\bfseries + \fi +} +\providecommand*{\beamer@bftext@warning}{% + \ClassWarning{beamer} + {Cannot use bold for alerted text in math mode}% +} + +\setbeamerfont{alerted text}{series=\beamer@bftext@only} + +\setbeamercolor{palette primary}{fg=karminrot,bg=white} +\setbeamercolor{palette secondary}{fg=gold,bg=white} +\setbeamercolor{palette tertiary}{fg=anthrazit,bg=white} +\setbeamercolor{palette quaternary}{fg=black,bg=white} + +\setbeamercolor{sidebar}{bg=karminrot!100} + +\setbeamercolor{palette sidebar primary}{fg=karminrot} +\setbeamercolor{palette sidebar secondary}{fg=karminrot} +\setbeamercolor{palette sidebar tertiary}{fg=karminrot} +\setbeamercolor{palette sidebar quaternary}{fg=karminrot} + +\setbeamercolor{item projected}{fg=black,bg=black!20} + +\setbeamercolor*{block body}{} +\setbeamercolor*{block body alerted}{} +\setbeamercolor*{block body example}{} +\setbeamercolor*{block title}{parent=structure} +\setbeamercolor*{block title alerted}{parent=alerted text} +\setbeamercolor*{block title example}{parent=example text} + +\setbeamercolor*{titlelike}{parent=structure} + +\mode + diff --git a/spike_trains/lecture/images/psth_comparison.pdf b/spike_trains/lecture/images/psth_comparison.pdf new file mode 100644 index 0000000..b9a5275 Binary files /dev/null and b/spike_trains/lecture/images/psth_comparison.pdf differ diff --git a/spike_trains/lecture/psth_sta.tex b/spike_trains/lecture/psth_sta.tex new file mode 100644 index 0000000..33bf2fb --- /dev/null +++ b/spike_trains/lecture/psth_sta.tex @@ -0,0 +1,36 @@ +\chapter{Spiketrainanalyse} + +Die zeitliche Abfolge von Aktionspotentialen, die ein Neuron generiert +enth\"alt die Information \"uber den Stimulus, die das Neuron +codiert. Aus der Analyse dieser Aktionspotentialfolgen oder, +kompakter, Spiketrains k\"onnen wir herausfinden welche Aspekte des +Stimulus codiert wird und somit nachfolgenden Verarbeitungsschritten +zur Verf\"ugung steht. + +Im elektrophysiologischen Experiment werden h\"aufig nur die +Zeitpunkte registriert an denen Aktionspotentiale, Spikes, +auftraten. Die Neuronale Aktivit\"at wird mitunter als Punktprozess +aufgefasst. Erstaunlicherweise lassen sich die Spiketrains mancher +kortikaler Neurone sehr gut durch ratenmodulierte Poissonprozesse +modellieren. + +Die Analyse von Spiketrains beinhaltet demnach einige der Methoden, +die auch f\"r die Beschreibung von Punktprozessen angewandt +werden. Dar\"uber hinaus wird versucht die Beziehung zwischen der +zeitabh\"aengigen neuronalen Antwort und dem zugrundeliegenden +Stimulus zu analysieren. + +\section{Darstellung der zeitabh\"angigen Feuerrate} + +Eine klassische Darstellung zeitabh\"angiger neuronaler Aktivit\"at +ist das sog. Peri Stimulus Zeithistogramm (peri stimulus time +histogram, PSTH). Es wird der zeitliche Verlauf der Feuerrate $r(t)$ +dargestellt. Die Einheit der Feuerrate ist Hertz, das heisst, die +Anzahl Aktionspotentiale pro Sekunde. Dabei gibt es verschiedene +Methoden diese zu bestimmen. Jede dieser Methoden hat ihre Vor- und +Nachteile. Abbildung \ref{psthfig} zeigt drei dieser Methoden. + +\begin{figure} + \includegraphics[width=0.75\columnwidth]{images/psth_comparison} + \caption{}\label{psthfig} +\end{figure} diff --git a/spike_trains/lecture/spike_trains-chapter.tex b/spike_trains/lecture/spike_trains-chapter.tex new file mode 100644 index 0000000..88ce960 --- /dev/null +++ b/spike_trains/lecture/spike_trains-chapter.tex @@ -0,0 +1,226 @@ +\documentclass[12pt]{report} + +%%%%% title %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\title{\tr{Introduction to Scientific Computing}{Einf\"uhrung in die wissenschaftliche Datenverarbeitung}} +\author{Jan Benda\\Abteilung Neuroethologie\\[2ex]\includegraphics[width=0.3\textwidth]{UT_WBMW_Rot_RGB}} +\date{WS 15/16} + +%%%% language %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% \newcommand{\tr}[2]{#1} % en +% \usepackage[english]{babel} +\newcommand{\tr}[2]{#2} % de +\usepackage[german]{babel} + +%%%%% packages 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references %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%\newcommand{\eqref}[1]{(\ref{#1})} +\newcommand{\eqn}{\tr{Eq}{Gl}.} +\newcommand{\Eqn}{\tr{Eq}{Gl}.} +\newcommand{\eqns}{\tr{Eqs}{Gln}.} +\newcommand{\Eqns}{\tr{Eqs}{Gln}.} +\newcommand{\eqnref}[1]{\eqn~\eqref{#1}} +\newcommand{\Eqnref}[1]{\Eqn~\eqref{#1}} +\newcommand{\eqnsref}[1]{\eqns~\eqref{#1}} +\newcommand{\Eqnsref}[1]{\Eqns~\eqref{#1}} + + +%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\usepackage{listings} +\lstset{ + inputpath=../code, + basicstyle=\ttfamily\footnotesize, + numbers=left, + showstringspaces=false, + language=Matlab, + commentstyle=\itshape\color{darkgray}, + keywordstyle=\color{blue}, + stringstyle=\color{green}, + backgroundcolor=\color{blue!10}, + breaklines=true, + breakautoindent=true, + columns=flexible, + frame=single, + caption={\protect\filename@parse{\lstname}\protect\filename@base}, + captionpos=t, + xleftmargin=1em, + xrightmargin=1em, + aboveskip=10pt +} + +%%%%% math stuff: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\usepackage{amsmath} +\usepackage{bm} +\usepackage{dsfont} +\newcommand{\naZ}{\mathds{N}} +\newcommand{\gaZ}{\mathds{Z}} +\newcommand{\raZ}{\mathds{Q}} +\newcommand{\reZ}{\mathds{R}} +\newcommand{\reZp}{\mathds{R^+}} +\newcommand{\reZpN}{\mathds{R^+_0}} +\newcommand{\koZ}{\mathds{C}} + + +%%%%% structure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\usepackage{ifthen} + +\newcommand{\code}[1]{\texttt{#1}} + +\newcommand{\source}[1]{ + \begin{flushright} + \color{gray}\scriptsize \url{#1} + \end{flushright} +} + +\newenvironment{definition}[1][]{\medskip\noindent\textbf{Definition}\ifthenelse{\equal{#1}{}}{}{ #1}:\newline}% + {\medskip} + +\newcounter{maxexercise} +\setcounter{maxexercise}{9} % show listings up to exercise maxexercise +\newcounter{theexercise} +\setcounter{theexercise}{1} +\newenvironment{exercise}[1][]{\medskip\noindent\textbf{\tr{Exercise}{\"Ubung} + \arabic{theexercise}:}\newline \newcommand{\exercisesource}{#1}}% + {\ifthenelse{\equal{\exercisesource}{}}{}{\ifthenelse{\value{theexercise}>\value{maxexercise}}{}{\medskip\lstinputlisting{\exercisesource}}}\medskip\stepcounter{theexercise}} + +\graphicspath{{figures/}} + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\begin{document} + +\include{psth_sta} + +\end{document} +