Commit ba334716 authored by Turnhout, M.C. van's avatar Turnhout, M.C. van
Browse files

Merge branch 'testing'

parents 1dbe36db dc611a36
# Version 0.031, collect more results
https://gitlab.tue.nl/STEM/DMAlab/tree/v0.031
* [update] add .fluo- and .bf-files to DMA_collectdir.m (as requested by Nikita :-) )
# Version 0.03, collect results, finish and add documentation # Version 0.03, collect results, finish and add documentation
https://gitlab.tue.nl/STEM/DMAlab/tree/v0.03 https://gitlab.tue.nl/STEM/DMAlab/tree/v0.03
......
...@@ -46,6 +46,24 @@ for s = 1:numel(param.collect) ...@@ -46,6 +46,24 @@ for s = 1:numel(param.collect)
elseif strcmp(param.collect{s}, 'dcel') elseif strcmp(param.collect{s}, 'dcel')
fprintf(fid, ['%i, %i, %i, %i, %i, %i, %i, %i, %i, ', ... fprintf(fid, ['%i, %i, %i, %i, %i, %i, %i, %i, %i, ', ...
'%i, %i, %i\n'], data'); '%i, %i, %i\n'], data');
elseif strcmp(param.collect{s}, 'fluo')
fprintf(fid, ['%1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%1.4e, %1.4e, %1.4e, %1.4e, %1.4e, %1.4e\n'], data');
elseif strcmp(param.collect{s}, 'bf')
fprintf(fid, ['%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e, ', ...
'%i, %1.4e, %1.4e, %1.4e, %1.4e\n'], data');
end end
end end
fclose(fid); fclose(fid);
......
...@@ -392,7 +392,7 @@ labdef = DMA_labconfig; % Courtesy of Douglas ...@@ -392,7 +392,7 @@ labdef = DMA_labconfig; % Courtesy of Douglas
labdef.maxgapw = 2; % only fill gaps when smaller than w frames labdef.maxgapw = 2; % only fill gaps when smaller than w frames
% collecting results % collecting results
labdef.collect = {'ncel', 'dcel'}; % extensions to collect labdef.collect = {'ncel', 'dcel', 'fluo', 'bf'}; % extensions to collect
%%% GUIs %%% %%% GUIs %%%
labdef.iscale = 100; % set cellminI threshhold in traceGUI at 100 pixels labdef.iscale = 100; % set cellminI threshhold in traceGUI at 100 pixels
...@@ -411,7 +411,7 @@ labdef = DMA_labconfig; % Courtesy of Douglas ...@@ -411,7 +411,7 @@ labdef = DMA_labconfig; % Courtesy of Douglas
% and finally: % and finally:
labdef.DMAlabUrl = 'https://gitlab.tue.nl/STEM/DMAlab'; labdef.DMAlabUrl = 'https://gitlab.tue.nl/STEM/DMAlab';
labdef.DMAlabBranch = 'master'; % Update to 'master' before merge! labdef.DMAlabBranch = 'master'; % Update to 'master' before merge!
labdef.DMAlabVersion = '0.03'; % Update *before* merge! labdef.DMAlabVersion = '0.031'; % Update *before* merge!
end end
......
...@@ -4,12 +4,13 @@ Feel it in the one drop; And we'll still find time to rap; \qauthor{Bob Marley \ ...@@ -4,12 +4,13 @@ Feel it in the one drop; And we'll still find time to rap; \qauthor{Bob Marley \
\end{savequote} \end{savequote}
\chapter{Under the hood}\label{hood} \chapter{Under the hood}\label{hood}
As mentioned in chapter \ref{workflow}, a image-stack analysis consists of four steps: droplet tracing (\texttt{BF}), fluorescence image pre-processing (\texttt{fluo}), cell counting (\texttt{ncel}) and events parsing (\texttt{dcel}). These steps are taken care of by \DMA{analyseFoV}: As mentioned in chapter \ref{workflow}, an image-stack analysis consists of four steps: droplet tracing (\texttt{BF}), fluorescence image pre-processing (\texttt{fluo}), cell counting (\texttt{ncel}) and events parsing (\texttt{dcel}). These steps are taken care of by \DMA{analyseFoV}:
\vspace*{-.4em}\begin{lstlisting}[language=DMAlab, numbers=none] \vspace*{-.4em}\begin{lstlisting}[language=DMAlab, numbers=none]
[BF, fluo, ncel, dcel] = DMA_analyseFoV; [BF, fluo, ncel, dcel] = DMA_analyseFoV;
\end{lstlisting} \end{lstlisting}
where \DMA{analyseFoV} calls \DMA{analyseevents} after the stack analysis to get \texttt{dcel}. where \DMA{analyseFoV} calls \DMA{analyseevents} after the stack analysis to get \texttt{dcel}.
In addition, it is possible to get an overview of the \texttt{ncel} and \texttt{dcel} results for the entire directory with image-stacks. This overview is created by \DMA{collectdir}.\\
In this chapter, we will briefly describe what \dmalab\ actually `does' in each step.\\ In this chapter, we will briefly describe what \dmalab\ actually `does' in each step.\\
...@@ -184,5 +185,5 @@ The area is assumed to be a circle with a certain radius so that the circles are ...@@ -184,5 +185,5 @@ The area is assumed to be a circle with a certain radius so that the circles are
\noindent \DMA{analyseevents} writes its results to the \texttt{dcel} file in \param{odir} (section \ref{outputdcel}). \noindent \DMA{analyseevents} writes its results to the \texttt{dcel} file in \param{odir} (section \ref{outputdcel}).
\section{Directory summary}
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