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--- a +++ b/talk/GrahamGroup.tex @@ -0,0 +1,1125 @@ + +% Default to the notebook output style + + + + +% Inherit from the specified cell style. + + + + + +\documentclass{article} + + + + \usepackage{graphicx} % Used to insert images + \usepackage{adjustbox} % Used to constrain images to a maximum size + \usepackage{color} % Allow colors to be defined + \usepackage{enumerate} % Needed for markdown enumerations to work + \usepackage{geometry} % Used to adjust the document margins + \usepackage{amsmath} % Equations + \usepackage{amssymb} % Equations + \usepackage[mathletters]{ucs} % Extended unicode (utf-8) support + \usepackage[utf8x]{inputenc} % Allow utf-8 characters in the tex document + \usepackage{fancyvrb} % verbatim replacement that allows latex + \usepackage{grffile} % extends the file name processing of package graphics + % to support a larger range + % The hyperref package gives us a pdf with properly built + % internal navigation ('pdf bookmarks' for the table of contents, + % internal cross-reference links, web links for URLs, etc.) + \usepackage{hyperref} + \usepackage{longtable} % longtable support required by pandoc >1.10 + \usepackage{booktabs} % table support for pandoc > 1.12.2 + + + + + \definecolor{orange}{cmyk}{0,0.4,0.8,0.2} + \definecolor{darkorange}{rgb}{.71,0.21,0.01} + \definecolor{darkgreen}{rgb}{.12,.54,.11} + \definecolor{myteal}{rgb}{.26, .44, .56} + \definecolor{gray}{gray}{0.45} + \definecolor{lightgray}{gray}{.95} + \definecolor{mediumgray}{gray}{.8} + \definecolor{inputbackground}{rgb}{.95, .95, .85} + \definecolor{outputbackground}{rgb}{.95, .95, .95} + \definecolor{traceback}{rgb}{1, .95, .95} + % ansi colors + \definecolor{red}{rgb}{.6,0,0} + \definecolor{green}{rgb}{0,.65,0} + \definecolor{brown}{rgb}{0.6,0.6,0} + \definecolor{blue}{rgb}{0,.145,.698} + \definecolor{purple}{rgb}{.698,.145,.698} + \definecolor{cyan}{rgb}{0,.698,.698} + \definecolor{lightgray}{gray}{0.5} + + % bright ansi colors + \definecolor{darkgray}{gray}{0.25} + \definecolor{lightred}{rgb}{1.0,0.39,0.28} + \definecolor{lightgreen}{rgb}{0.48,0.99,0.0} + \definecolor{lightblue}{rgb}{0.53,0.81,0.92} + \definecolor{lightpurple}{rgb}{0.87,0.63,0.87} + \definecolor{lightcyan}{rgb}{0.5,1.0,0.83} + + % commands and environments needed by pandoc snippets + % extracted from the output of `pandoc -s` + \DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}} + % Add ',fontsize=\small' for more characters per line + \newenvironment{Shaded}{}{} + \newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}} + \newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{{#1}}} + \newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}} + \newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}} + \newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}} + \newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}} + \newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}} + \newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{{#1}}}} + \newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{{#1}}} + \newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}} + \newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{{#1}}} + \newcommand{\RegionMarkerTok}[1]{{#1}} + \newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}} + \newcommand{\NormalTok}[1]{{#1}} + + % Define a nice break command that doesn't care if a line doesn't already + % exist. + \def\br{\hspace*{\fill} \\* } + % Math Jax compatability definitions + \def\gt{>} + \def\lt{<} + % Document parameters + \title{GrahamGroup} + + + + + % Pygments definitions + +\makeatletter +\def\PY@reset{\let\PY@it=\relax \let\PY@bf=\relax% + \let\PY@ul=\relax \let\PY@tc=\relax% + \let\PY@bc=\relax \let\PY@ff=\relax} +\def\PY@tok#1{\csname PY@tok@#1\endcsname} +\def\PY@toks#1+{\ifx\relax#1\empty\else% + \PY@tok{#1}\expandafter\PY@toks\fi} +\def\PY@do#1{\PY@bc{\PY@tc{\PY@ul{% + \PY@it{\PY@bf{\PY@ff{#1}}}}}}} +\def\PY#1#2{\PY@reset\PY@toks#1+\relax+\PY@do{#2}} + +\expandafter\def\csname PY@tok@gd\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}} +\expandafter\def\csname PY@tok@gu\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}} +\expandafter\def\csname PY@tok@gt\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}} +\expandafter\def\csname PY@tok@gs\endcsname{\let\PY@bf=\textbf} +\expandafter\def\csname PY@tok@gr\endcsname{\def\PY@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}} +\expandafter\def\csname PY@tok@cm\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} +\expandafter\def\csname PY@tok@vg\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} +\expandafter\def\csname PY@tok@m\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@mh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@go\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.53,0.53,0.53}{##1}}} +\expandafter\def\csname PY@tok@ge\endcsname{\let\PY@it=\textit} +\expandafter\def\csname PY@tok@vc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} +\expandafter\def\csname PY@tok@il\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@cs\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} +\expandafter\def\csname PY@tok@cp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.74,0.48,0.00}{##1}}} +\expandafter\def\csname PY@tok@gi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}} +\expandafter\def\csname PY@tok@gh\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}} +\expandafter\def\csname PY@tok@ni\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.60,0.60,0.60}{##1}}} +\expandafter\def\csname 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PY@tok@si\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}} +\expandafter\def\csname PY@tok@s2\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} +\expandafter\def\csname PY@tok@vi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} +\expandafter\def\csname PY@tok@nt\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@nv\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} +\expandafter\def\csname PY@tok@s1\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} +\expandafter\def\csname PY@tok@sh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} +\expandafter\def\csname PY@tok@sc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} +\expandafter\def\csname PY@tok@sx\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@bp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@c1\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} +\expandafter\def\csname PY@tok@kc\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@c\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} +\expandafter\def\csname PY@tok@mf\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@err\endcsname{\def\PY@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}} +\expandafter\def\csname PY@tok@kd\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@ss\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} +\expandafter\def\csname PY@tok@sr\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}} +\expandafter\def\csname PY@tok@mo\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@kn\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@mi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@gp\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}} +\expandafter\def\csname PY@tok@o\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} +\expandafter\def\csname PY@tok@kr\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@s\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} +\expandafter\def\csname PY@tok@kp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@w\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}} +\expandafter\def\csname PY@tok@kt\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.69,0.00,0.25}{##1}}} +\expandafter\def\csname PY@tok@ow\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}} +\expandafter\def\csname PY@tok@sb\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} +\expandafter\def\csname PY@tok@k\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} +\expandafter\def\csname PY@tok@se\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.13}{##1}}} +\expandafter\def\csname PY@tok@sd\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} + +\def\PYZbs{\char`\\} +\def\PYZus{\char`\_} +\def\PYZob{\char`\{} +\def\PYZcb{\char`\}} +\def\PYZca{\char`\^} +\def\PYZam{\char`\&} +\def\PYZlt{\char`\<} +\def\PYZgt{\char`\>} +\def\PYZsh{\char`\#} +\def\PYZpc{\char`\%} +\def\PYZdl{\char`\$} +\def\PYZhy{\char`\-} +\def\PYZsq{\char`\'} +\def\PYZdq{\char`\"} +\def\PYZti{\char`\~} +% for compatibility with earlier versions +\def\PYZat{@} +\def\PYZlb{[} +\def\PYZrb{]} +\makeatother + + + % Exact colors from NB + \definecolor{incolor}{rgb}{0.0, 0.0, 0.5} + \definecolor{outcolor}{rgb}{0.545, 0.0, 0.0} + + + + + % Prevent overflowing lines due to hard-to-break entities + \sloppy + % Setup hyperref package + \hypersetup{ + breaklinks=true, % so long urls are correctly broken across lines + colorlinks=true, + urlcolor=blue, + linkcolor=darkorange, + citecolor=darkgreen, + } + % Slightly bigger margins than the latex defaults + + \geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in} + + + + \begin{document} + + + \maketitle + + + + + + \section{Robust Extraction of Quantitative Information from Histology Images} + + + + \paragraph{Quentin Caudron Romain Garnier \emph{with Bryan Grenfell and Andrea +Graham}} + + + + \subsubsection{Outline} + + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + Image processing +\item + Extracted measures +\item + Preliminary analysis +\item + Future directions +\end{itemize} + + \begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\setcounter{enumi}{3} +\itemsep1pt\parskip0pt\parsep0pt +\item + Age as random effect \textless{}--- +\end{enumerate} + +{[}``interface\_hepatitis'', ``confluent\_necrosis'', +``portal\_inflammation'', ``ln\_ap\_ri''{]} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}3}]:} \PY{k}{def} \PY{n+nf}{normalise}\PY{p}{(}\PY{n}{df}\PY{p}{,} \PY{n}{skip} \PY{o}{=} \PY{p}{[}\PY{p}{]}\PY{p}{)} \PY{p}{:} + \PY{k}{for} \PY{n}{i} \PY{o+ow}{in} \PY{n}{df}\PY{o}{.}\PY{n}{columns} \PY{p}{:} + \PY{k}{if} \PY{n}{i} \PY{o+ow}{not} \PY{o+ow}{in} \PY{n}{skip} \PY{p}{:} + \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]} \PY{o}{\PYZhy{}}\PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]}\PY{o}{.}\PY{n}{mean}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]} \PY{o}{/}\PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]}\PY{o}{.}\PY{n}{std}\PY{p}{(}\PY{p}{)} + \PY{k}{return} \PY{n}{df} + + + + + + + \PY{k}{def} \PY{n+nf}{rescale}\PY{p}{(}\PY{n}{df}\PY{p}{,} \PY{n}{skip} \PY{o}{=} \PY{p}{[}\PY{p}{]}\PY{p}{)} \PY{p}{:} + \PY{k}{for} \PY{n}{i} \PY{o+ow}{in} \PY{n}{df}\PY{o}{.}\PY{n}{columns} \PY{p}{:} + \PY{k}{if} \PY{n}{i} \PY{o+ow}{not} \PY{o+ow}{in} \PY{n}{skip} \PY{p}{:} + \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]} \PY{o}{\PYZhy{}}\PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]}\PY{o}{.}\PY{n}{min}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]} \PY{o}{/}\PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{n}{i}\PY{p}{]}\PY{o}{.}\PY{n}{max}\PY{p}{(}\PY{p}{)} + \PY{k}{return} \PY{n}{df} + + + + \PY{c}{\PYZsh{} Remove a layer from a list} + \PY{k}{def} \PY{n+nf}{delayer}\PY{p}{(}\PY{n}{m}\PY{p}{)} \PY{p}{:} + \PY{n}{out} \PY{o}{=} \PY{p}{[}\PY{p}{]} + \PY{k}{for} \PY{n}{i} \PY{o+ow}{in} \PY{n}{m} \PY{p}{:} + \PY{k}{if} \PY{n+nb}{isinstance}\PY{p}{(}\PY{n}{i}\PY{p}{,} \PY{n+nb}{list}\PY{p}{)} \PY{p}{:} + \PY{k}{for} \PY{n}{j} \PY{o+ow}{in} \PY{n}{i} \PY{p}{:} + \PY{n}{out}\PY{o}{.}\PY{n}{append}\PY{p}{(}\PY{n}{j}\PY{p}{)} + \PY{k}{else} \PY{p}{:} + \PY{n}{out}\PY{o}{.}\PY{n}{append}\PY{p}{(}\PY{n}{i}\PY{p}{)} + \PY{k}{return} \PY{n}{out} + + + + + + + + \PY{c}{\PYZsh{} Remove all layers from a list} + \PY{k}{def} \PY{n+nf}{flatten}\PY{p}{(}\PY{n}{m}\PY{p}{)} \PY{p}{:} + \PY{n}{out} \PY{o}{=} \PY{n}{m}\PY{p}{[}\PY{p}{:}\PY{p}{]} + + \PY{k}{while} \PY{n}{out} \PY{o}{!=} \PY{n}{delayer}\PY{p}{(}\PY{n}{out}\PY{p}{)} \PY{p}{:} + \PY{n}{out} \PY{o}{=} \PY{n}{delayer}\PY{p}{(}\PY{n}{out}\PY{p}{)} + + \PY{k}{return} \PY{n}{out} + + + + + + + + + \PY{c}{\PYZsh{} Generate all combinations of objects in a list} + \PY{k}{def} \PY{n+nf}{combinatorial}\PY{p}{(}\PY{n}{l}\PY{p}{)} \PY{p}{:} + \PY{n}{out} \PY{o}{=} \PY{p}{[}\PY{p}{]} + + \PY{k}{for} \PY{n}{numel} \PY{o+ow}{in} \PY{n+nb}{range}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{l}\PY{p}{)}\PY{p}{)} \PY{p}{:} + \PY{k}{for} \PY{n}{i} \PY{o+ow}{in} \PY{n}{itertools}\PY{o}{.}\PY{n}{combinations}\PY{p}{(}\PY{n}{l}\PY{p}{,} \PY{n}{numel}\PY{o}{+}\PY{l+m+mi}{1}\PY{p}{)} \PY{p}{:} + \PY{n}{out}\PY{o}{.}\PY{n}{append}\PY{p}{(}\PY{n+nb}{list}\PY{p}{(}\PY{n}{i}\PY{p}{)}\PY{p}{)} + + \PY{k}{return} \PY{n}{out} + + + + + + + + + + + \PY{k}{def} \PY{n+nf}{pcaplot}\PY{p}{(}\PY{n}{df}\PY{p}{)} \PY{p}{:} + + \PY{c}{\PYZsh{} PCA} + \PY{n}{pca} \PY{o}{=} \PY{n}{decomposition}\PY{o}{.}\PY{n}{PCA}\PY{p}{(}\PY{n}{whiten} \PY{o}{=} \PY{n+nb+bp}{True}\PY{p}{)} + \PY{n}{pca}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{n}{df}\PY{p}{)} + \PY{n}{p1} \PY{o}{=} \PY{n}{pca}\PY{o}{.}\PY{n}{components\PYZus{}}\PY{p}{[}\PY{l+m+mi}{0}\PY{p}{]} \PY{o}{/} \PY{n}{np}\PY{o}{.}\PY{n}{abs}\PY{p}{(}\PY{n}{pca}\PY{o}{.}\PY{n}{components\PYZus{}}\PY{p}{[}\PY{l+m+mi}{0}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{max}\PY{p}{(}\PY{p}{)} \PY{o}{*} \PY{n}{np}\PY{o}{.}\PY{n}{sqrt}\PY{p}{(}\PY{l+m+mi}{2}\PY{p}{)}\PY{o}{/}\PY{l+m+mi}{2} + \PY{n}{p2} \PY{o}{=} \PY{n}{pca}\PY{o}{.}\PY{n}{components\PYZus{}}\PY{p}{[}\PY{l+m+mi}{1}\PY{p}{]} \PY{o}{/} \PY{n}{np}\PY{o}{.}\PY{n}{abs}\PY{p}{(}\PY{n}{pca}\PY{o}{.}\PY{n}{components\PYZus{}}\PY{p}{[}\PY{l+m+mi}{1}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{max}\PY{p}{(}\PY{p}{)} \PY{o}{*} \PY{n}{np}\PY{o}{.}\PY{n}{sqrt}\PY{p}{(}\PY{l+m+mi}{2}\PY{p}{)}\PY{o}{/}\PY{l+m+mi}{2} + + \PY{c}{\PYZsh{} Normalise} + \PY{n}{norms} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{max}\PY{p}{(}\PY{p}{[}\PY{n}{np}\PY{o}{.}\PY{n}{sqrt}\PY{p}{(}\PY{p}{(}\PY{n}{np}\PY{o}{.}\PY{n}{array}\PY{p}{(}\PY{n+nb}{zip}\PY{p}{(}\PY{n}{p1}\PY{p}{,} \PY{n}{p2}\PY{p}{)}\PY{p}{[}\PY{n}{i}\PY{p}{]}\PY{p}{)}\PY{o}{*}\PY{o}{*}\PY{l+m+mi}{2}\PY{p}{)}\PY{o}{.}\PY{n}{sum}\PY{p}{(}\PY{p}{)}\PY{p}{)} \PY{k}{for} \PY{n}{i} \PY{o+ow}{in} \PY{n+nb}{range}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{p1}\PY{p}{)}\PY{p}{)}\PY{p}{]}\PY{p}{)} + \PY{n}{c} \PY{o}{=} \PY{n}{plt}\PY{o}{.}\PY{n}{Circle}\PY{p}{(} \PY{p}{(}\PY{l+m+mi}{0}\PY{p}{,} \PY{l+m+mi}{0}\PY{p}{)}\PY{p}{,} \PY{n}{radius} \PY{o}{=} \PY{l+m+mi}{1}\PY{p}{,} \PY{n}{alpha} \PY{o}{=} 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\PY{l+s}{\PYZdq{}}\PY{l+s}{Directionality}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{o}{.}\PY{n}{dropna}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{ones}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{df}\PY{p}{)}\PY{p}{)} + \PY{n}{maxhepsize} \PY{o}{=} \PY{n}{sm}\PY{o}{.}\PY{n}{GLS}\PY{p}{(}\PY{n}{endog} \PY{o}{=} \PY{n}{df}\PY{o}{.}\PY{n}{Max\PYZus{}hep\PYZus{}size}\PY{p}{,} \PY{n}{exog} \PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Entropy}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Directionality}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{p}{)}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{maxhepsize}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} + + + + + \PY{n}{df} \PY{o}{=} \PY{n}{age}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Lobular\PYZus{}collapse}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{FociSize}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{o}{.}\PY{n}{dropna}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{ones}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{df}\PY{p}{)}\PY{p}{)} + \PY{n}{lobular\PYZus{}collapse} \PY{o}{=} \PY{n}{sm}\PY{o}{.}\PY{n}{GLS}\PY{p}{(}\PY{n}{endog} \PY{o}{=} \PY{n}{df}\PY{o}{.}\PY{n}{Lobular\PYZus{}collapse}\PY{p}{,} \PY{n}{exog} \PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{FociSize}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{p}{)}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{lobular\PYZus{}collapse}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} + + + \PY{n}{df} \PY{o}{=} \PY{n}{age}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Interface\PYZus{}hepatitis}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Lacunarity}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{o}{.}\PY{n}{dropna}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{ones}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{df}\PY{p}{)}\PY{p}{)} + \PY{n}{interface\PYZus{}hepatitis} \PY{o}{=} \PY{n}{sm}\PY{o}{.}\PY{n}{GLS}\PY{p}{(}\PY{n}{endog} \PY{o}{=} \PY{n}{df}\PY{o}{.}\PY{n}{Interface\PYZus{}hepatitis}\PY{p}{,} \PY{n}{exog} \PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Lacunarity}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{p}{)}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{interface\PYZus{}hepatitis}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} + + + \PY{n}{df} \PY{o}{=} \PY{n}{age}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Fibrosis}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Inflammation}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{o}{.}\PY{n}{dropna}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{ones}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{df}\PY{p}{)}\PY{p}{)} + \PY{n}{fibrosis} \PY{o}{=} \PY{n}{sm}\PY{o}{.}\PY{n}{GLS}\PY{p}{(}\PY{n}{endog} \PY{o}{=} \PY{n}{df}\PY{o}{.}\PY{n}{Fibrosis}\PY{p}{,} \PY{n}{exog} \PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Inflammation}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{p}{)}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{fibrosis}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} + + + + + \PY{c}{\PYZsh{} PCA} + + \PY{n}{s} \PY{o}{=} \PY{n}{sheep}\PY{o}{.}\PY{n}{dropna}\PY{p}{(}\PY{n}{subset}\PY{o}{=}\PY{n}{delayer}\PY{p}{(}\PY{p}{[}\PY{n}{imagecols}\PY{p}{,} \PY{n}{histcols}\PY{p}{]}\PY{p}{)}\PY{p}{)} + \PY{n}{pca} \PY{o}{=} \PY{n}{decomposition}\PY{o}{.}\PY{n}{PCA}\PY{p}{(}\PY{n}{n\PYZus{}components}\PY{o}{=}\PY{l+m+mi}{1}\PY{p}{)} + \PY{n}{pcax} \PY{o}{=} \PY{n}{pca}\PY{o}{.}\PY{n}{fit\PYZus{}transform}\PY{p}{(}\PY{n}{s}\PY{p}{[}\PY{n}{imagecols}\PY{p}{]}\PY{p}{)} + \PY{n}{pcay} \PY{o}{=} \PY{n}{pca}\PY{o}{.}\PY{n}{fit\PYZus{}transform}\PY{p}{(}\PY{n}{s}\PY{p}{[}\PY{n}{histcols}\PY{p}{]}\PY{p}{)} + \PY{n}{pca} \PY{o}{=} \PY{n}{sm}\PY{o}{.}\PY{n}{GLS}\PY{p}{(}\PY{n}{endog} \PY{o}{=} \PY{n}{pcay}\PY{p}{[}\PY{p}{:}\PY{p}{,} \PY{l+m+mi}{0}\PY{p}{]}\PY{p}{[}\PY{p}{:}\PY{p}{,} \PY{n}{np}\PY{o}{.}\PY{n}{newaxis}\PY{p}{]}\PY{p}{,} \PY{n}{exog} \PY{o}{=} \PY{n}{add\PYZus{}constant}\PY{p}{(}\PY{n}{pcax}\PY{p}{)}\PY{p}{)}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{p}{)}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{pca}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} + + + + + + \PY{c}{\PYZsh{} REGRESSIONS : mixed effects, intercept on age at death} + + \PY{n}{df} \PY{o}{=} \PY{n}{age}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Fibrosis}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Inflammation}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{o}{.}\PY{n}{dropna}\PY{p}{(}\PY{p}{)} + \PY{n}{df}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{ones}\PY{p}{(}\PY{n+nb}{len}\PY{p}{(}\PY{n}{df}\PY{p}{)}\PY{p}{)} + \PY{n}{fibrosis} \PY{o}{=} \PY{n}{sm}\PY{o}{.}\PY{n}{GLS}\PY{p}{(}\PY{n}{endog} \PY{o}{=} \PY{n}{df}\PY{o}{.}\PY{n}{Fibrosis}\PY{p}{,} \PY{n}{exog} \PY{o}{=} \PY{n}{df}\PY{p}{[}\PY{p}{[}\PY{l+s}{\PYZdq{}}\PY{l+s}{Inflammation}\PY{l+s}{\PYZdq{}}\PY{p}{,} \PY{l+s}{\PYZdq{}}\PY{l+s}{Intercept}\PY{l+s}{\PYZdq{}}\PY{p}{]}\PY{p}{]}\PY{p}{)}\PY{o}{.}\PY{n}{fit}\PY{p}{(}\PY{p}{)}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{fibrosis}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}19}]:} \PY{n}{a} \PY{o}{=} \PY{n}{portal\PYZus{}inflammation}\PY{o}{.}\PY{n}{summary}\PY{p}{(}\PY{p}{)} + \PY{k}{del} \PY{n}{a}\PY{o}{.}\PY{n}{tables}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]} + \PY{n}{a} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}19}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + =============================================================================== + Dep. Variable: Portal\_inflammation R-squared: 0.280 + Model: GLS Adj. R-squared: 0.273 + Method: Least Squares F-statistic: 37.34 + Date: Tue, 28 Oct 2014 Prob (F-statistic): 2.12e-08 + Time: 23:35:30 Log-Likelihood: 14.996 + No. Observations: 98 AIC: -25.99 + Df Residuals: 96 BIC: -20.82 + Df Model: 1 + Covariance Type: nonrobust + ============================================================================== + coef std err t P>|t| [95.0\% Conf. Int.] + ------------------------------------------------------------------------------ + FociSize 0.5627 0.092 6.111 0.000 0.380 0.746 + Intercept 0.3368 0.043 7.855 0.000 0.252 0.422 + ============================================================================== + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + + \subsection{Image Processing} + + + + + + + + \subsubsection{Extraction} + + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + Automagical +\item + Reasonably quick +\end{itemize} + + + \subsubsection{Robust} + + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + Invariant to staining, slicing, field-related variation +\item + Capture intersample variation +\end{itemize} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/robust3.jpg} +\caption{image} +\end{figure} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/robust4.jpg} +\caption{image} +\end{figure} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/robust1.jpg} +\caption{image} +\end{figure} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/robust2.jpg} +\caption{image} +\end{figure} + + + \subsection{Structural and Textural Measures} + + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + characteristic \textbf{scale} of sinusoid widths +\item + \textbf{directional} amplitude of preferred sinusoid alignment +\item + \textbf{tissue to sinusoid} ratio +\item + \textbf{count} of inflammatory foci per image +\item + \textbf{mean size} of inflammatory foci per image +\item + information \textbf{entropy} of sinusoid distribution +\item + \textbf{lacunarity} ( clustering ) of sinusoids +\end{itemize} + + + + \begin{figure}[htbp] +\centering +\includegraphics{figures/intra.png} +\caption{image} +\end{figure} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/inter2.png} +\caption{image} +\end{figure} + + + \subsection{Exploratory Analysis} + + + + \subsubsection{by individual} + + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}29}]:} \PY{n}{portal\PYZus{}inflammation} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}29}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + =============================================================================== + Dep. Variable: Portal\_inflammation R-squared: 0.280 + Model: GLS Adj. R-squared: 0.273 + Method: Least Squares F-statistic: 37.34 + Date: Tue, 28 Oct 2014 Prob (F-statistic): 2.12e-08 + Time: 23:40:10 Log-Likelihood: 14.996 + No. Observations: 98 AIC: -25.99 + Df Residuals: 96 BIC: -20.82 + Df Model: 1 + Covariance Type: nonrobust + ============================================================================== + coef std err t P>|t| [95.0\% Conf. Int.] + ------------------------------------------------------------------------------ + FociSize 0.5627 0.092 6.111 0.000 0.380 0.746 + Intercept 0.3368 0.043 7.855 0.000 0.252 0.422 + ============================================================================== + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/portal_inflammation.png} +\caption{image} +\end{figure} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}31}]:} \PY{n}{hyperplasia} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}31}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + ============================================================================== + Dep. Variable: BD\_hyperplasia R-squared: 0.306 + Model: GLS Adj. R-squared: 0.284 + Method: Least Squares F-statistic: 13.83 + Date: Tue, 28 Oct 2014 Prob (F-statistic): 1.52e-07 + Time: 23:40:10 Log-Likelihood: -3.9632 + No. Observations: 98 AIC: 15.93 + Df Residuals: 94 BIC: 26.27 + Df Model: 3 + Covariance Type: nonrobust + ================================================================================== + coef std err t P>|t| [95.0\% Conf. Int.] + ---------------------------------------------------------------------------------- + FociSize 0.6698 0.113 5.902 0.000 0.444 0.895 + Scale 0.5811 0.243 2.394 0.019 0.099 1.063 + Directionality -0.4419 0.190 -2.330 0.022 -0.819 -0.065 + Intercept -0.0504 0.079 -0.642 0.523 -0.206 0.105 + ================================================================================== + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/hyperplasia.png} +\caption{image} +\end{figure} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}15}]:} \PY{n}{pca} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}15}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + ============================================================================== + Dep. Variable: y R-squared: 0.075 + Model: GLS Adj. R-squared: 0.065 + Method: Least Squares F-statistic: 7.723 + Date: Wed, 29 Oct 2014 Prob (F-statistic): 0.00657 + Time: 14:38:47 Log-Likelihood: -70.082 + No. Observations: 97 AIC: 144.2 + Df Residuals: 95 BIC: 149.3 + Df Model: 1 + Covariance Type: nonrobust + ============================================================================== + coef std err t P>|t| [95.0\% Conf. Int.] + ------------------------------------------------------------------------------ + const -2.949e-17 0.051 -5.77e-16 1.000 -0.102 0.102 + x1 0.3865 0.139 2.779 0.007 0.110 0.663 + ============================================================================== + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/pca.png} +\caption{image} +\end{figure} + + + \subsection{Exploratory Analysis} + + + + \subsubsection{by age class} + + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}6}]:} \PY{n}{fibrosis} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}6}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + ============================================================================== + Dep. Variable: Fibrosis R-squared: 0.800 + Model: GLS Adj. R-squared: 0.778 + Method: Least Squares F-statistic: 36.07 + Date: Wed, 29 Oct 2014 Prob (F-statistic): 0.000201 + Time: 11:13:48 Log-Likelihood: 7.8003 + No. Observations: 11 AIC: -11.60 + Df Residuals: 9 BIC: -10.80 + Df Model: 1 + Covariance Type: nonrobust + ================================================================================ + coef std err t P>|t| [95.0\% Conf. Int.] + -------------------------------------------------------------------------------- + Inflammation 1.0159 0.169 6.006 0.000 0.633 1.399 + Intercept -0.0105 0.083 -0.126 0.902 -0.198 0.177 + ================================================================================ + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/fibrosis.png} +\caption{image} +\end{figure} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}7}]:} \PY{n}{lobular\PYZus{}collapse} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}7}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + ============================================================================== + Dep. Variable: Lobular\_collapse R-squared: 0.586 + Model: GLS Adj. R-squared: 0.540 + Method: Least Squares F-statistic: 12.73 + Date: Wed, 29 Oct 2014 Prob (F-statistic): 0.00605 + Time: 11:13:48 Log-Likelihood: 2.2626 + No. Observations: 11 AIC: -0.5252 + Df Residuals: 9 BIC: 0.2706 + Df Model: 1 + Covariance Type: nonrobust + ============================================================================== + coef std err t P>|t| [95.0\% Conf. Int.] + ------------------------------------------------------------------------------ + FociSize 1.1379 0.319 3.567 0.006 0.416 1.860 + Intercept 0.0460 0.159 0.289 0.779 -0.314 0.406 + ============================================================================== + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/lobular_collapse.png} +\caption{image} +\end{figure} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{incolor}In [{\color{incolor}8}]:} \PY{n}{interface\PYZus{}hepatitis} +\end{Verbatim} + + \begin{Verbatim}[commandchars=\\\{\}] +{\color{outcolor}Out[{\color{outcolor}8}]:} <class 'statsmodels.iolib.summary.Summary'> + """ + GLS Regression Results + =============================================================================== + Dep. Variable: Interface\_hepatitis R-squared: 0.659 + Model: GLS Adj. R-squared: 0.621 + Method: Least Squares F-statistic: 17.38 + Date: Wed, 29 Oct 2014 Prob (F-statistic): 0.00242 + Time: 11:13:48 Log-Likelihood: 2.3063 + No. Observations: 11 AIC: -0.6126 + Df Residuals: 9 BIC: 0.1832 + Df Model: 1 + Covariance Type: nonrobust + ============================================================================== + coef std err t P>|t| [95.0\% Conf. Int.] + ------------------------------------------------------------------------------ + Lacunarity -1.0224 0.245 -4.168 0.002 -1.577 -0.468 + Intercept 0.9504 0.143 6.669 0.000 0.628 1.273 + ============================================================================== + + Warnings: + [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. + """ +\end{Verbatim} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/interface_hepatitis.png} +\caption{image} +\end{figure} + + + \subsection{Exploratory analysis} + + + + \subsubsection{with a random effect on age at death} + + + \begin{longtable}[c]{@{}lcl@{}} +\toprule\addlinespace +Dependent variable & Models AIC \textless{} 2 + AICmin & Primary +explanatory variables ( ordered ) +\\\addlinespace +\midrule\endhead +Ishak score & 7 & entropy, tissue-to-sinusoid, focus count, focus size +\\\addlinespace +Lobular collapse & 5 & entropy, lacunarity, tissue-to-sinusoid, focus +count +\\\addlinespace +Confluent necrosis & 1 & entropy +\\\addlinespace +Interface hepatitis & 2 & entropy, tissue-to-sinusoid +\\\addlinespace +Portal inflammation & 4 & entropy, focus size, lacunarity, focus count, +scale, directionality +\\\addlinespace +Fibrosis & 2 & entropy, lacunarity, tissue-to-sinusoid +\\\addlinespace +Biliary hyperplasia & 1 & focus size +\\\addlinespace +Necrosis, apoptosis, random inflammation & 2 & entropy, lacunarity +\\\addlinespace +\bottomrule +\end{longtable} + + + \paragraph{Measures we like} + + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + entropy consistently explains histological measures when controlled + for age +\item + also important : tissue to sinusoid ratio, focus count and size, + lacunarity +\end{itemize} + + + \subsection{Future directions} + + + + \subsubsection{Further exploration of the dataset} + + + \begin{itemize} +\item + 145 sheep ( 89 females ) +\item + 11 age classes +\item +\end{itemize} + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + 4460 entries across 27 variables +\item + 3330 with full image and histological information +\item + 1196 for which \textbf{complete} information is available +\end{itemize} + + + \subsubsection{Narrow-field images} + + + \begin{itemize} +\itemsep1pt\parskip0pt\parsep0pt +\item + 12536 images +\item + spatial distribution of nuclei +\end{itemize} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/10.jpg} +\caption{image} +\end{figure} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/Processed2.jpg} +\caption{image} +\end{figure} + + \begin{figure}[htbp] +\centering +\includegraphics{figures/Segmented.jpg} +\caption{image} +\end{figure} + + + + + % Add a bibliography block to the postdoc + + + + \end{document}