Commit 43fc2a64 authored by Turnhout, M.C. van's avatar Turnhout, M.C. van
Browse files

reorganise repository

parent 35ceb718
.gitattributes export-ignore
.gitignore export-ignore
/documentation export-ignore
/data export-ignore
DMAlab.pdf -diff
......@@ -38,8 +38,11 @@ Thumbs.db
# Linux git ignore
.*
!.gitignore
*~
!.gitignore
!.gitattributes
!documentation/pics/*.pdf
##---------------------------------------------------
......
......@@ -122,8 +122,8 @@ uicontrol('Parent', framepanel, 'Style', 'pushbutton', 'Position', ...
panelpos = updatepanelpos(panelpos);
lpanelpos = panelpos;
lpanelpos(3) = lpanelpos(3)-lpanelpos(3)/2-5;
japos = imresize( imread(fullfile(DMA_labpath, 'pics/JApos.png')), [25 75])/2;
janeg = imresize( imread(fullfile(DMA_labpath, 'pics/JAneg.png')), [25 75])/2;
japos = imresize( imread(fullfile(DMA_labpath, 'gui/JApos.png')), [25 75])/2;
janeg = imresize( imread(fullfile(DMA_labpath, 'gui/JAneg.png')), [25 75])/2;
acceptpanel = uipanel( 'Title', 'Accept and ...', ...
'BackgroundColor', 'white', 'units', 'pixel', 'Position', lpanelpos);
......@@ -140,7 +140,7 @@ quitpanel = uipanel( 'Title', 'do not accept and ...', ...
'BackgroundColor', 'white', 'units', 'pixel', 'Position', rpanelpos);
uicontrol('Parent', quitpanel, 'Style', 'pushbutton', 'Cdata', japos, ...
'Position', [5 5 75 25], 'String', 'reset', 'ForegroundColor', [1 1 1]', 'Callback', @Qreset);
bg = imresize( imread(fullfile(DMA_labpath, 'pics/Flag_of_Ethiopia.png')), [25 50]);
bg = imresize( imread(fullfile(DMA_labpath, 'gui/Flag_of_Ethiopia.png')), [25 50]);
uicontrol('Parent', quitpanel, 'Style', 'pushbutton', 'ForegroundColor', [1 1 1]', ...
'Cdata', bg, 'Position', [210 5 50 25], 'String', 'exit', 'Callback', @Qquit);
......
......@@ -136,7 +136,7 @@ uicontrol('Parent', droppanel, 'Style', 'pushbutton', 'Position', ...
buttonpos(3, :), 'BackgroundColor', [0 1 0], ...
'String', 'random droplet', 'Callback', @droprandbutton);
% interactive select
bg = imresize( imread(fullfile(DMA_labpath, 'pics/Flag_of_Jamaica.png')), [25 50]);
bg = imresize( imread(fullfile(DMA_labpath, 'gui/Flag_of_Jamaica.png')), [25 50]);
uicontrol('Parent', droppanel, 'Style', 'pushbutton', 'Position', ...
[490 5 50 25], 'Cdata', bg, ...
'String', 'pick', 'Foregroundcolor', [1 1 1], 'Callback', @droppickbutton);
......@@ -191,8 +191,8 @@ uicontrol('Parent', chpanel, 'Style', 'pushbutton', 'Position', ...
panelpos = updatepanelpos(panelpos);
lpanelpos = panelpos;
lpanelpos(3) = lpanelpos(3)-lpanelpos(3)/2-5;
japos = imresize( imread(fullfile(DMA_labpath, 'pics/JApos.png')), [25 75])/2;
janeg = imresize( imread(fullfile(DMA_labpath, 'pics/JAneg.png')), [25 75])/2;
japos = imresize( imread(fullfile(DMA_labpath, 'gui/JApos.png')), [25 75])/2;
janeg = imresize( imread(fullfile(DMA_labpath, 'gui/JAneg.png')), [25 75])/2;
acceptpanel = uipanel( 'Title', 'Accept and ...', ...
'BackgroundColor', 'white', 'units', 'pixel', 'Position', lpanelpos);
......@@ -207,7 +207,7 @@ quitpanel = uipanel( 'Title', 'do not accept and ...', ...
'BackgroundColor', 'white', 'units', 'pixel', 'Position', rpanelpos);
uicontrol('Parent', quitpanel, 'Style', 'pushbutton', 'Cdata', japos, ...
'Position', [5 5 75 25], 'String', 'reset', 'ForegroundColor', [1 1 1]', 'Callback', @Qreset);
bg = imresize( imread(fullfile(DMA_labpath, 'pics/Flag_of_Ethiopia.png')), [25 50]);
bg = imresize( imread(fullfile(DMA_labpath, 'gui/Flag_of_Ethiopia.png')), [25 50]);
uicontrol('Parent', quitpanel, 'Style', 'pushbutton', 'ForegroundColor', [1 1 1]', ...
'Cdata', bg, 'Position', [210 5 50 25], 'String', 'exit', 'Callback', @Qquit);
......
......@@ -160,7 +160,7 @@ uicontrol('Parent', droppanel, 'Style', 'pushbutton', 'Position', ...
%%% second row
% interactive select
bg = imresize( imread(fullfile(DMA_labpath, ...
'pics/Flag_of_Jamaica.png')), [25 50]);
'gui/Flag_of_Jamaica.png')), [25 50]);
uicontrol('Parent', droppanel, 'Style', 'pushbutton', 'Position', ...
numpos-[0 35 0 0], 'Cdata', bg, 'String', 'pick', ...
'Foregroundcolor', [1 1 1], 'Callback', @droppickbutton);
......@@ -218,7 +218,7 @@ elseif style == 4
end
% go to parameter settings button
bg = imresize( imread(fullfile(DMA_labpath, ...
'pics/Flag_of_Ethiopia.png')), [50 100]);
'gui/Flag_of_Ethiopia.png')), [50 100]);
uicontrol('Parent', fluopanel, 'Style', 'pushbutton', 'Position', ...
[buttonpos(3, 1)+50 10 100 50], 'Cdata', bg, ...
'String', 'go to settings', 'Foregroundcolor', [0 0 0], ...
......
......@@ -41,7 +41,7 @@
% graphics, figures, colour
\usepackage[pdftex]{graphicx}
\graphicspath{{../pics/}}
\graphicspath{{pics/}}
\usepackage{transparent}
\usepackage{xcolor}
\definecolor{shadecolor}{rgb}{0.95,0.95,0.95}
......
......@@ -20,17 +20,17 @@ We perform our fluorescence analysis on individual `droplets' that first need to
\begin{figure}[p]
\subfloat[ \texttt{raw} \label{contrasta}]{%
\includegraphics[width=0.4\linewidth]{../pics/contrasta.png}}\hfill
\includegraphics[width=0.4\linewidth]{pics/contrasta.png}}\hfill
\subfloat[237 detected droplets in \textbf{(a)}\label{contrastb}]{%
\includegraphics[width=0.4\linewidth]{../pics/contrastb.png}}\\
\includegraphics[width=0.4\linewidth]{pics/contrastb.png}}\\
\subfloat[ \texttt{imadjust(raw, [0.01 0.4])} \label{contrastc}]{%
\includegraphics[width=0.4\linewidth]{../pics/contrastc.png}}\hfill
\includegraphics[width=0.4\linewidth]{pics/contrastc.png}}\hfill
\subfloat[239 detected droplets in \textbf{(c)}\label{contrastd}]{%
\includegraphics[width=0.4\linewidth]{../pics/contrastd.png}}\\
\includegraphics[width=0.4\linewidth]{pics/contrastd.png}}\\
\subfloat[ \texttt{imadjust(raw, [], [], 0.4)} \label{contraste}]{%
\includegraphics[width=0.4\linewidth]{../pics/contraste.png}}\hfill
\includegraphics[width=0.4\linewidth]{pics/contraste.png}}\hfill
\subfloat[242 detected droplets in \textbf{(e)}\label{contrastf}]{%
\includegraphics[width=0.4\linewidth]{../pics/contrastf.png}}\\
\includegraphics[width=0.4\linewidth]{pics/contrastf.png}}\\
\caption{Contrast stretching can improve droplet detection. With \textbf{(a)} the raw image is rather dark, and \textbf{(b)} we can detect a mere 237\,droplets; \textbf{(c)} strong linear contrast stretching brightens the image relative to the dark circles we wish to detect, and \textbf{(d)} results in 239 detected droplets; and \textbf{(e)} strong non-linear contrast stretching with default moderate limits ([0.01 0.99]) also brightens the image, and \textbf{(f)} results in an impressive 242 detected droplets.\label{contrastexample}}
\end{figure}
......@@ -53,9 +53,9 @@ The results contain the $x$- and $y$-coordinates of the centres of the detected
\begin{figure}[t!]
\subfloat[\label{droplettracinga}]{%
\includegraphics[width=0.47\linewidth]{../pics/fig_droplettracinga.png}}\hfill
\includegraphics[width=0.47\linewidth]{pics/fig_droplettracinga.png}}\hfill
\subfloat[\label{droplettracingb}]{%
\includegraphics[width=0.485\linewidth]{../pics/fig_droplettracingb.png}}\\
\includegraphics[width=0.485\linewidth]{pics/fig_droplettracingb.png}}\\
\caption{Droplet detection on brightfield images with Matlab's \href{https://www.mathworks.com/help/images/ref/imfindcircles.html}{imfindcircles.m}. With \textbf{(a)} the raw brightfield data, and \textbf{(b)} an overlay with detected circles (blue) and their index number. Index numbers are red for droplets that will not be taken into account because they touch the image border, and green otherwise. \\ Note that those index numbers do not seem to follow any sensible pattern. \label{fig_droplettracing}}
\end{figure}
......@@ -111,13 +111,13 @@ We apply a threshold in the fourth step (figure \ref{fluoprocessd}) based on \pa
\begin{figure}[tb!]
\subfloat[\label{fluoprocessa}]{%
\includegraphics[width=0.47\linewidth]{../pics/fig_fluoprocessa.png}}\hfill
\includegraphics[width=0.47\linewidth]{pics/fig_fluoprocessa.png}}\hfill
\subfloat[\label{fluoprocessb}]{%
\includegraphics[width=0.47\linewidth]{../pics/fig_fluoprocessb.png}}\\
\includegraphics[width=0.47\linewidth]{pics/fig_fluoprocessb.png}}\\
\subfloat[\label{fluoprocessc}]{%
\includegraphics[width=0.47\linewidth]{../pics/fig_fluoprocessc.png}}\hfill
\includegraphics[width=0.47\linewidth]{pics/fig_fluoprocessc.png}}\hfill
\subfloat[\label{fluoprocessd}]{%
\includegraphics[width=0.47\linewidth]{../pics/fig_fluoprocessd.png}}\\
\includegraphics[width=0.47\linewidth]{pics/fig_fluoprocessd.png}}\\
\caption{The four steps of fluorescence image processing, with \textbf{(a)} crop to droplet, \textbf{(b)} apply top-hat filter, \textbf{(c)} dismiss non-droplet pixels, and \textbf{(d)} apply a threshold to identify the objects. \label{figfluoprocess}}
\end{figure}
......
......@@ -19,16 +19,16 @@ DMA_tracedroplet('/home/mark/tue/log/191031_druppels/k562activated002_002_004.ti
\end{lstlisting}
This will produce three overview images for the data in the \texttt{.bf}-, \texttt{.fluo}- and \texttt{.ncel}-files (figure \ref{tracedropletbfline}).
\begin{figure}[h]
\subfloat[\label{tracedropleta}]{\includegraphics[width=0.32\linewidth]{../pics/fig_tracedropleta.png}}\hfill
\subfloat[\label{tracedroplete}]{\includegraphics[width=0.32\linewidth]{../pics/fig_tracedroplete.png}}\hfill
\subfloat[\label{tracedropletf}]{\includegraphics[width=0.32\linewidth]{../pics/fig_tracedropletf.png}}\\
\subfloat[\label{tracedropleta}]{\includegraphics[width=0.32\linewidth]{pics/fig_tracedropleta.png}}\hfill
\subfloat[\label{tracedroplete}]{\includegraphics[width=0.32\linewidth]{pics/fig_tracedroplete.png}}\hfill
\subfloat[\label{tracedropletf}]{\includegraphics[width=0.32\linewidth]{pics/fig_tracedropletf.png}}\\
\caption{Three droplet tracing figures. With \textbf{(a)} The brightfield image of the first time point superimposed with the detected circles for the chosen droplet for each time point (from the \texttt{.bf}-file); \textbf{(b)} the mean intensities from the \texttt{.fluo}-file for this droplet (for each fluorescence channel), and \textbf{(c)} the cell counts from the \texttt{.ncel}-file for this droplet (for each fluorescence channel).\\ Not to scale. See also figure \ref{tracedropletfluo}.\label{tracedropletbfline}}
\end{figure}
\begin{figure}[p]
\center
\subfloat[\label{tracedropletb}]{\includegraphics[width=.95\linewidth]{../pics/fig_tracedropletb.png}}\\
\subfloat[\label{tracedropletc}]{\includegraphics[width=.95\linewidth]{../pics/fig_tracedropletc.png}}\\
\subfloat[\label{tracedropletd}]{\includegraphics[width=.95\linewidth]{../pics/fig_tracedropletd.png}}\\
\subfloat[\label{tracedropletb}]{\includegraphics[width=.95\linewidth]{pics/fig_tracedropletb.png}}\\
\subfloat[\label{tracedropletc}]{\includegraphics[width=.95\linewidth]{pics/fig_tracedropletc.png}}\\
\subfloat[\label{tracedropletd}]{\includegraphics[width=.95\linewidth]{pics/fig_tracedropletd.png}}\\
\caption{Three droplet tracing figures for three fluorescence channels. See also figure \ref{tracedropletbfline}.\label{tracedropletfluo}}
\end{figure}
......@@ -55,9 +55,9 @@ The function \DMA{traceGUI} (figure \ref{figtracegui}) has been present since ve
\begin{figure}[h]
\subfloat[\label{traceguioverview}]{%
\includegraphics[width=0.47\linewidth]{../pics/traceguioverview.png}}\hfill
\includegraphics[width=0.47\linewidth]{pics/traceguioverview.png}}\hfill
\subfloat[\label{traceguigui}]{%
\includegraphics[width=0.47\linewidth]{../pics/traceguigui.png}}\\
\includegraphics[width=0.47\linewidth]{pics/traceguigui.png}}\\
\caption{The \DMA{traceGUI} GUI. With \textbf({a}) the overview figure with the four images for the current time point of the current image stack (1 brightfield image and three fluorescence images), and \textbf{(b)} the control GUI figure (not to scale). \label{figtracegui}}
\end{figure}
......@@ -97,9 +97,9 @@ The function \DMA{setfluoparam} allows you to validate and adjust cell detection
\begin{figure}[b!]
\subfloat[\label{setfluooverview}]{%
\includegraphics[width=0.47\linewidth]{../pics/setfluoparamoverview.png}}\hfill
\includegraphics[width=0.47\linewidth]{pics/setfluoparamoverview.png}}\hfill
\subfloat[\label{setfluoGUI}]{%
\includegraphics[width=0.47\linewidth]{../pics/setfluoparamgui.png}}\\
\includegraphics[width=0.47\linewidth]{pics/setfluoparamgui.png}}\\
\caption{The \DMA{setfluoparam} GUI. With \textbf({a}) the overview figure with results based on the current settings (column for each fluorescence channel), and \textbf{(b)} the control GUI figure (not to scale either). \label{figsetfluoparam}}
\end{figure}
......@@ -145,9 +145,9 @@ The function \DMA{setBFparam} allows you to validate and adjust droplet detectio
\begin{figure}[b!]
\subfloat[\label{setBFoverview}]{%
\includegraphics[width=0.48\linewidth]{../pics/setBFparamoverview.png}}\hfill
\includegraphics[width=0.48\linewidth]{pics/setBFparamoverview.png}}\hfill
\subfloat[\label{setBFGUI}]{%
\includegraphics[width=0.46\linewidth]{../pics/setBFparamGUI.png}}\\
\includegraphics[width=0.46\linewidth]{pics/setBFparamGUI.png}}\\
\caption{The \DMA{setBFparam} GUI. With \textbf({a}) the overview figure with results based on the current settings, and \textbf{(b)} the control GUI figure (still not to scale). \label{figsetBFparam}}
\end{figure}
......
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