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SynD_aggregate.m
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% Synapse Detector (SynD)
%
% Johannes Hjorth
%
% Sabine Schmitz
%
function SynD_aggregate()
close all
data = [];
conserveMemory = 1;
groupIdx = []; % Index of group each neuron belongs to
% Group info structure
group = struct('Name',[], ...
'Members', []);
morphLabel = 'MAP2';
synLabel = 'VAMP2';
XLabel = 'Munc18';
exportFileMask = '%s-export-summary.xml';
exportFile = [];
exportPath = pwd;
loadPath = pwd;
plotDir = [];
plotExperimentName = [];
configFile = strrep(mfilename('fullpath'), ...
mfilename(), ...
'SynD_aggregate_config.mat');
versionFile = strrep(mfilename('fullpath'), ...
mfilename(), ...
'version.txt');
loadConfig();
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
handles.fig = figure('Name','SynD - Aggregate data (also known as BarB)', ...
'MenuBar','none', ...
'Toolbar','none', ...
'Position', [50 50 1150 680]);
handles.plot = axes('Units','Pixels', 'Position', [660 250 400 400]);
% !!! Disabled hotkeys
%set(handles.fig,'WindowKeyPressFcn',@captureKeyPress);
handles.selectData = uicontrol('Style','listbox', ...
'String', 'None', ...
'ToolTipString', ...
'Choose data to group', ...
'Value', [1], ...
'Max', 1, 'Min', 1, ...
'Interruptible', 'off', ...
'Callback', @dataListboxClicked, ...
'Position',[50 50 380 600]);
handles.groupNameLabel = uicontrol('Style', 'text', ...
'String', 'Group name:', ...
'HorizontalAlignment','left', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [450 620 100 25]);
handles.groupName = uicontrol('Style','edit', ...
'String', 'WT', ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [450 595 150 30]);
handles.morphNameLabel = uicontrol('Style', 'text', ...
'String', 'Morph marker:', ...
'HorizontalAlignment','left', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [450 560 100 25]);
handles.morphName = uicontrol('Style','edit', ...
'String', morphLabel, ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [450 535 150 30], ...
'Callback', @updateLabels);
handles.synNameLabel = uicontrol('Style', 'text', ...
'String', 'Synapse marker:', ...
'HorizontalAlignment','left', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [450 500 100 25]);
handles.synName = uicontrol('Style','edit', ...
'String', synLabel, ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [450 475 150 30], ...
'Callback', @updateLabels);
handles.XNameLabel = uicontrol('Style', 'text', ...
'String', 'X marker:', ...
'HorizontalAlignment','left', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [450 440 100 25]);
handles.XName = uicontrol('Style','edit', ...
'String', XLabel, ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [450 415 150 30], ...
'Callback', @updateLabels);
handles.makeGroup = uicontrol('Style','pushbutton', ...
'String','<html><u>D</u>efine group</html>', ...
'Interruptible', 'off', ...
'Position',[450,360,100,30], ...
'Callback', @defineGroup);
handles.guessGroup = uicontrol('Style','pushbutton', ...
'String','<html>Find</html>', ...
'fontsize', 8, ...
'Interruptible', 'off', ...
'Position',[560,370,40,20], ...
'Callback', @guessGroup);
handles.makeGroup = uicontrol('Style','pushbutton', ...
'String','<html><u>E</u>xport data</html>', ...
'Interruptible', 'off', ...
'Position',[450,320,100,30], ...
'Callback', @exportData);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
handles.plotTypeLabel = uicontrol('Style','text', ...
'String', 'Show plot:', ...
'HorizontalAlignment', 'left', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [660 180 100 30]);
handles.plotType = uicontrol('Style','popupmenu', ...
'String', {'Plot type list'}, ...
'fontsize', 10, ...
'Position', [660 160 350 30], ...
'Value', 1, ...
'Callback', @showPlot);
handles.saveAllPlots = uicontrol('Style','pushbutton', ...
'String','Save all plots', ...
'Interruptible', 'off', ...
'Position',[740,120,100,30], ...
'Callback', @saveAllPlots);
handles.savePlot = uicontrol('Style','pushbutton', ...
'String','Save plot', ...
'Interruptible', 'off', ...
'Position',[660,120,70,30], ...
'Callback', @savePlotCallback);
handles.saveSummaryPlots = uicontrol('Style','pushbutton', ...
'String','Save summary plots', ...
'Interruptible', 'off', ...
'Position',[850,120,140,30], ...
'Callback', @makeAllSummaryPlots);
saveFileType = {'eps','pdf','png'};
handles.fileType = uicontrol('Style','popupmenu', ...
'String', saveFileType, ...
'fontsize', 10, ...
'Position', [1020 160 70 30], ...
'Value', 1);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for iGB = 1:12
boxX = mod(iGB-1,4);
boxY = 2-floor((iGB-1)/4);
handles.groupLabels(iGB) = uicontrol('Style','text', ...
'String',num2str(iGB), ...
'BackgroundColor', 0.8*[1 1 1], ...
'HorizontalAlignment','right', ...
'Fontsize', 8, ...
'Visible', 'off', ...
'Position', ...
[455+40*boxX 230+30*boxY 20 10]);
handles.groupBox(iGB) = uicontrol('Style','checkbox', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Visible', 'off', ...
'Value', 0, ...
'Position', ...
[475+40*boxX 225+30*boxY 20 20], ...
'Callback', @selectGroups);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
handles.XlimMinLabel = uicontrol('Style', 'text', ...
'String', 'Xmin', ...
'Fontsize',7, ...
'HorizontalAlignment','center', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [450 200 40 15]);
handles.XlimMaxLabel = uicontrol('Style', 'text', ...
'String', 'Xmax', ...
'Fontsize',7, ...
'HorizontalAlignment','center', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [490 200 40 15]);
handles.YlimMinLabel = uicontrol('Style', 'text', ...
'String', 'Ymin', ...
'Fontsize',7, ...
'HorizontalAlignment','center', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [530 200 40 15]);
handles.YlimMaxLabel = uicontrol('Style', 'text', ...
'String', 'Ymax', ...
'Fontsize',7, ...
'HorizontalAlignment','center', ...
'BackgroundColor', 0.8*[1 1 1], ...
'Position', [570 200 40 15]);
handles.XlimMin = uicontrol('Style','edit', ...
'String', '', ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [450 175 40 30]);
handles.XlimMax = uicontrol('Style','edit', ...
'String', '', ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [490 175 40 30]);
handles.YlimMin = uicontrol('Style','edit', ...
'String', '', ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [530 175 40 30]);
handles.YlimMax = uicontrol('Style','edit', ...
'String', '', ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'Position', [570 175 40 30]);
handles.setAxis = uicontrol('Style','pushbutton', ...
'String','Change axis', ...
'Interruptible', 'off', ...
'Position',[450,130,100,30], ...
'Callback', @setAxis);
handles.barGraphDotsText = uicontrol('Style', 'text', ...
'String', 'Bar graph dots:', ...
'Fontsize', 12, ...
'BackgroundColor', 0.8*[1 1 1], ...
'HorizontalAlignment','left', ...
'Position', [450 100 110 20]);
handles.barGraphDots = uicontrol('Style', 'checkbox', ...
'Value', 0, 'Max', 1, ...
'BackgroundColor', 0.8*[1 1 1], ...
'Interruptible', 'off', ...
'Enable', 'off', ...
'Position', [560 100 20 20], ...
'Callback', @setBarGraphDots);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
handles.menuFile = uimenu(handles.fig,'Label','File');
handles.menuItemLoad = uimenu(handles.menuFile, ...
'Label','Load data', ...
'Interruptible','off', ...
'Callback', @loadData);
handles.menuItemLoad = uimenu(handles.menuFile, ...
'Label','Export data', ...
'Interruptible','off', ...
'Callback', @exportData);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
handles.menuDebug = uimenu(handles.fig,'Label','Debug');
handles.menuItemDebug = uimenu(handles.menuDebug, ...
'Label','Keyboard', ...
'Interruptible', 'off', ...
'Callback', @runDebug);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function runDebug(source, event)
disp('Type return to exit debug mode')
keyboard
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
plotInfo = struct('PlotName', [], ...
'PlotType', [], ...
'DataStr', [], ...
'Xlabel', [], ...
'Ylabel', [], ...
'FigName', [], ...
'barGraphDots', 0, ...
'Xlim', [], ...
'Ylim', []);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function setPlotInfo()
% "Basics"
% 2) synapse number: Bar graph
% y-axis: Mean synapse number
% x-axis: (empty)
plotInfo(1).Name = 'Synapse number';
plotInfo(1).Type = 'bar';
plotInfo(1).DataStr = 'nSynapses';
plotInfo(1).Xlabel = '';
plotInfo(1).Ylabel = 'Mean synapse number';
plotInfo(1).FigName = 'synapse_number';
plotInfo(1).barGraphDots = 1;
% 3)Total dendrite length: Bar graph
% y-axis: Mean total dendrite length (um)
% x-axis: (empty)
% Apologies, the totDendLength is NOT in SI units... sorry.
% Sabine comment: it is in micrometers.
% Update: is is in meters...
plotInfo(2).Name = 'Dendritic length';
plotInfo(2).Type = 'bar';
plotInfo(2).DataStr = 'totDendLength*1e6';
plotInfo(2).Xlabel = '';
plotInfo(2).Ylabel = 'Mean total dendrite length (\mum)';
plotInfo(2).FigName = 'total_dendrite_length';
plotInfo(2).barGraphDots = 1;
% 4) synapse number/dendrite length: Bar graph
% y-axis: Mean synapse number per um dendrite
% x-axis: (empty)
plotInfo(3).Name = 'Synapse number/Dendritic length';
plotInfo(3).Type = 'bar';
plotInfo(3).DataStr = {'nSynapses', 'totDendLength*1e6'};
plotInfo(3).Xlabel = '';
plotInfo(3).Ylabel = 'Mean synapses number per \mum dendrite';
plotInfo(3).FigName = 'synapse_number_per__dendrite_length';
plotInfo(3).barGraphDots = 1;
% 5) synapse size: Bar graph
% y-axis: Mean synapse area (um2)
% x-axis: (empty)
plotInfo(4).Name = 'Mean synapse area';
plotInfo(4).Type = 'bar';
plotInfo(4).DataStr = 'synapseArea'; % This is already in micrometers...
plotInfo(4).Xlabel = '';
plotInfo(4).Ylabel = 'Mean synapse area (\mum^2)';
plotInfo(4).FigName = 'synapse_area';
plotInfo(4).barGraphDots = 1;
% 6) synaptic morphology intensity: Bar graph
% y-axis: Mean synaptic morphology intensity (a.u.)
% x-axis: (empty)
plotInfo(5).Name = sprintf('Synaptic %s intensity', morphLabel);
plotInfo(5).Type = 'bar';
plotInfo(5).DataStr = 'synapseIntensityMorphMean';
plotInfo(5).Xlabel = '';
plotInfo(5).Ylabel = sprintf('Mean synaptic %s intensity (a.u.)',morphLabel);
plotInfo(5).FigName = sprintf('synaptic_%s_intensity', morphLabel);
plotInfo(5).barGraphDots = 1;
% 7) synapse intensity: Bar graph
% y-axis: Mean synapse intensity (a.u.)
% x-axis: (empty)
plotInfo(6).Name = sprintf('Synaptic %s intensity', synLabel);
plotInfo(6).Type = 'bar';
plotInfo(6).DataStr = 'synapseIntensitySynMean';
plotInfo(6).Xlabel = '';
plotInfo(6).Ylabel = sprintf('Mean synaptic %s intensity (a.u.)', synLabel);
plotInfo(6).FigName = sprintf('synaptic_%s_intensity', synLabel);
plotInfo(6).barGraphDots = 1;
% 8) synaptic X intensity: Bar graph
% y-axis: Mean synaptic X intensity (a.u.)
% x-axis: (empty)
plotInfo(7).Name = sprintf('Synaptic %s intensity', XLabel);
plotInfo(7).Type = 'bar';
plotInfo(7).DataStr = 'synapseIntensityXMean';
plotInfo(7).Xlabel = '';
plotInfo(7).Ylabel = sprintf('Mean synaptic %s intensity (a.u.)',XLabel);
plotInfo(7).FigName = sprintf('synaptic_%s_intensity', XLabel);
plotInfo(7).barGraphDots = 1;
% 9) synaptic synapse/morphology intensity: Bar graph
% y-axis: Mean synaptic synapse/morphology intensity (a.u.)
% x-axis: (empty)
plotInfo(8).Name = sprintf('Synaptic %s/%s intensity', synLabel,morphLabel);
plotInfo(8).Type = 'bar';
plotInfo(8).DataStr = {'synapseIntensitySynMean','synapseIntensityMorphMean'};
plotInfo(8).Xlabel = '';
plotInfo(8).Ylabel = sprintf('Mean synaptic %s/%s intensity (a.u.)', ...
synLabel, morphLabel);
plotInfo(8).FigName = sprintf('synaptic_ratio_of_%s_and_%s_intensity', ...
synLabel, morphLabel);
plotInfo(8).barGraphDots = 1;
% 10) synaptic X/morphology intensity: Bar graph
% y-axis: Mean synapse intensity (a.u.)
% x-axis: (empty)
plotInfo(9).Name = sprintf('Synaptic %s/%s intensity', XLabel,morphLabel);
plotInfo(9).Type = 'bar';
plotInfo(9).DataStr = {'synapseIntensityXMean','synapseIntensityMorphMean'};
plotInfo(9).Xlabel = '';
plotInfo(9).Ylabel = sprintf('Mean synaptic %s/%s intensity (a.u.)', ...
XLabel, morphLabel);
plotInfo(9).FigName = sprintf('synaptic_ratio_of_%s_and_%s_intensity', ...
XLabel, morphLabel);
plotInfo(9).barGraphDots = 1;
% 11) synaptic X/synapse intensity: Bar graph
% y-axis: Mean synaptic X/synapse intensity (a.u.)
% x-axis: (empty)
plotInfo(10).Name = sprintf('Synaptic %s/%s intensity', XLabel,synLabel);
plotInfo(10).Type = 'bar';
plotInfo(10).DataStr = {'synapseIntensityXMean','synapseIntensitySynMean'};
plotInfo(10).Xlabel = '';
plotInfo(10).Ylabel = sprintf('Mean synaptic %s/%s intensity (a.u.)', ...
XLabel, synLabel);
plotInfo(10).FigName = sprintf('synaptic_ratio_of_%s_and_%s_intensity', ...
XLabel, synLabel);
plotInfo(10).barGraphDots = 1;
% 13) somatic morphology intensity: Bar graph
% y-axis: Mean somatic morphology intensity (a.u.)
% x-axis: (empty)
plotInfo(11).Name = sprintf('Somatic %s intensity', morphLabel);
plotInfo(11).Type = 'bar';
plotInfo(11).DataStr = 'somaMeasureMorph';
plotInfo(11).Xlabel = '';
plotInfo(11).Ylabel = sprintf('Mean somatic %s intensity (a.u.)', morphLabel);
plotInfo(11).FigName = sprintf('somatic_%s_intensity',morphLabel);
plotInfo(11).barGraphDots = 1;
% 14) somatic synapse intensity: Bar graph
% y-axis: Mean somatic synapse intensity (a.u.)
% x-axis: (empty)
plotInfo(12).Name = sprintf('Somatic %s intensity', synLabel);
plotInfo(12).Type = 'bar';
plotInfo(12).DataStr = 'somaMeasureSyn';
plotInfo(12).Xlabel = '';
plotInfo(12).Ylabel = sprintf('Mean somatic %s intensity (a.u.)', synLabel);
plotInfo(12).FigName = sprintf('somatic_%s_intensity',synLabel);
plotInfo(12).barGraphDots = 1;
% 15) somatic X intensity: Bar graph
% y-axis: Mean somatic X intensity (a.u.)
% x-axis: (empty)
plotInfo(13).Name = sprintf('Somatic %s intensity', XLabel);
plotInfo(13).Type = 'bar';
plotInfo(13).DataStr = 'somaMeasureX';
plotInfo(13).Xlabel = '';
plotInfo(13).Ylabel = sprintf('Mean somatic %s intensity (a.u.)',XLabel);
plotInfo(13).FigName = sprintf('somatic_%s_intensity',XLabel);
plotInfo(13).barGraphDots = 1;
% 16) soma area: Bar graph
% y-axis: Mean soma area (um2)
% x-axis: (empty)
plotInfo(14).Name = 'Soma area';
plotInfo(14).Type = 'bar';
plotInfo(14).DataStr = 'somaArea';
plotInfo(14).Xlabel = '';
plotInfo(14).Ylabel = 'Mean soma area (\mum^2)';
plotInfo(14).FigName = 'soma_area';
plotInfo(14).barGraphDots = 1;
% 17) major soma axis: Bar graph
% y-axis: Mean major soma axis (um2)
% x-axis: (empty)
plotInfo(15).Name = 'Soma major axis';
plotInfo(15).Type = 'bar';
plotInfo(15).DataStr = 'somaMajorAxisLength';
plotInfo(15).Xlabel = '';
plotInfo(15).Ylabel = 'Soma major axis (\mum)';
plotInfo(15).FigName = 'soma_major_axis';
plotInfo(15).barGraphDots = 1;
% 18) minor soma axis: Bar graph
% y-axis: Mean minor soma axis (um2)
% x-axis: (empty)
plotInfo(16).Name = 'Soma minor axis';
plotInfo(16).Type = 'bar';
plotInfo(16).DataStr = 'somaMinorAxisLength';
plotInfo(16).Xlabel = '';
plotInfo(16).Ylabel = 'Soma minor axis (\mum)';
plotInfo(16).FigName = 'soma_minor_axis';
plotInfo(16).barGraphDots = 1;
% 19) synaptic/somatic morphology intensity: Bar graph
% y-axis: Mean synaptic/somatic morphology intensity (a.u.)
% x-axis: (empty)
plotInfo(17).Name = sprintf('Synaptic/somatic %s intensity', morphLabel);
plotInfo(17).Type = 'bar';
plotInfo(17).DataStr = {'synapseIntensityMorphMean', 'somaMeasureMorph'};
plotInfo(17).Xlabel = '';
plotInfo(17).Ylabel = sprintf('Mean synaptic/somatic %s intensity', morphLabel);
plotInfo(17).FigName = sprintf('synaptic_to_somatic_%s_intensity_ratio',morphLabel);
plotInfo(17).barGraphDots = 1;
% 20) synaptic/somatic synapse intensity: Bar graph
% y-axis: Mean synaptic/somatic synapse intensity (a.u.)
% x-axis: (empty)
plotInfo(18).Name = sprintf('Synaptic/somatic %s intensity', synLabel);
plotInfo(18).Type = 'bar';
plotInfo(18).DataStr = {'synapseIntensitySynMean', 'somaMeasureSyn'};
plotInfo(18).Xlabel = '';
plotInfo(18).Ylabel = sprintf('Mean synaptic/somatic %s intensity', synLabel);
plotInfo(18).FigName = sprintf('synaptic_to_somatic_%s_intensity_ratio', synLabel);
plotInfo(18).barGraphDots = 1;
% 21) synaptic/somatic X intensity: Bar graph
% y-axis: Mean synaptic/somatic X intensity (a.u.)
% x-axis: (empty)
plotInfo(19).Name = sprintf('Synaptic/somatic %s intensity', XLabel);
plotInfo(19).Type = 'bar';
plotInfo(19).DataStr = {'synapseIntensityXMean', 'somaMeasureX'};
plotInfo(19).Xlabel = '';
plotInfo(19).Ylabel = sprintf('Mean synaptic/somatic %s intensity', XLabel);
plotInfo(19).FigName = sprintf('synaptic_to_somatic_%s_intensity_ratio', XLabel);
plotInfo(19).barGraphDots = 1;
% 22) synaptic/somatic (synapse/morphology) intensity: Bar graph
% y-axis: Mean synaptic/somatic (synapse/morphology) intensity (a.u.)
% x-axis: (empty)
plotInfo(20).Name = sprintf('Synaptic %s/somatic %s intensity', ...
synLabel, morphLabel);
plotInfo(20).Type = 'bar';
plotInfo(20).DataStr = {'synapseIntensitySynMean', 'somaMeasureMorph'};
plotInfo(20).Xlabel = '';
plotInfo(20).Ylabel = sprintf('Mean synaptic %s/somatic %s intensity', ...
synLabel, morphLabel);
plotInfo(20).FigName = sprintf('synaptic_%s_to_somatic_%s_intensity_ratio', ...
synLabel, morphLabel);
plotInfo(20).barGraphDots = 1;
% 23) synaptic/somatic (X/morphology) intensity: Bar graph
% y-axis: Mean synaptic/somatic (X/morphology) intensity (a.u.)
% x-axis: (empty)
plotInfo(21).Name = sprintf('Synaptic %s/somatic %s intensity', ...
XLabel, morphLabel);
plotInfo(21).Type = 'bar';
plotInfo(21).DataStr = {'synapseIntensityXMean', 'somaMeasureMorph'};
plotInfo(21).Xlabel = '';
plotInfo(21).Ylabel = sprintf('Mean synaptic %s/somatic %s intensity', ...
XLabel, morphLabel);
plotInfo(21).FigName = sprintf('synaptic_%s_to_somatic_%s_intensity_ratio', ...
XLabel, morphLabel);
plotInfo(21).barGraphDots = 1;
% 24) synaptic/somatic (X/synapse) intensity: Bar graph
% y-axis: Mean synaptic/somatic (X/synapse) intensity (a.u.)
% x-axis: (empty)
plotInfo(22).Name = sprintf('Synaptic %s/somatic %s intensity', ...
XLabel, synLabel);
plotInfo(22).Type = 'bar';
plotInfo(22).DataStr = {'synapseIntensityXMean', 'somaMeasureSyn'};
plotInfo(22).Xlabel = '';
plotInfo(22).Ylabel = sprintf('Mean synaptic %s/somatic %s intensity', ...
XLabel, synLabel);
plotInfo(22).FigName = sprintf('synaptic_%s_to_somatic_%s_intensity_ratio', ...
XLabel, synLabel);
plotInfo(22).barGraphDots = 1;
%"M"
% n) cumulative histogram of synaptic morphology intensity: cumulative histogram (see supplementary Fig.4 SynD paper)
% y-axis: cumulative probability (%)
% x-axis: distance from soma (um)
plotInfo(23).Name = sprintf('Cumulative histogram of synaptic %s intensity', ...
morphLabel);
plotInfo(23).Type = 'cumhist';
plotInfo(23).DataStr = 'morphHist';
plotInfo(23).Xlabel = 'Fluorescent intensity (a.u.)';
plotInfo(23).Ylabel = 'Cumulative probability (%)';
plotInfo(23).FigName = sprintf('cumulative_histogram_synaptic_%s_intensity', ...
morphLabel);
% "S"
% n) cumulative histogram of synapse intensity: cumulative histogram
% y-axis: cumulative probability (%)
% x-axis: distance from soma (um)
plotInfo(24).Name = sprintf('Cumulative histogram of synaptic %s intensity', ...
synLabel);
plotInfo(24).Type = 'cumhist';
plotInfo(24).DataStr = 'synHist';
plotInfo(24).Xlabel = 'Fluorescent intensity (a.u.)';
plotInfo(24).Ylabel = 'Cumulative probability (%)';
plotInfo(24).FigName = sprintf('cumulative_histogram_synaptic_%s_intensity', ...
synLabel);
% "X"
% n) cumulative histogram of synaptic X intensity: cumulative histogram
% y-axis: cumulative probability (%)
% x-axis: distance from soma (um)
plotInfo(25).Name = sprintf('Cumulative histogram of synaptic %s intensity', ...
XLabel);
plotInfo(25).Type = 'cumhist';
plotInfo(25).DataStr = 'XHist';
plotInfo(25).Xlabel = 'Fluorescent intensity (a.u.)';
plotInfo(25).Ylabel = 'Cumulative probability (%)';
plotInfo(25).FigName = sprintf('cumulative_histogram_synaptic_%s_intensity', ...
XLabel);
% "Sholl dend"
% n) Sholl analysis: Histogram (connected points, see Fig3B SynD paper)
% y-axis: number of branches
% x-axis: distance from soma (um)
plotInfo(26).Name = 'Sholl analysis';
plotInfo(26).Type = 'hist';
plotInfo(26).DataStr = 'DendHist';
plotInfo(26).Xlabel = 'Distance from soma (\mum)';
plotInfo(26).Ylabel = 'Mean number of branches';
plotInfo(26).FigName = 'sholl_dendrite_analysis';
% "Sholl synd"
% n) Synapse localization: Histogram (as bars, see Fig3C SynD paper)
% y-axis: number of synapses
% x-axis: distance from soma (um)
plotInfo(27).Name = 'Synapse localisation';
plotInfo(27).Type = 'hist';
plotInfo(27).DataStr = 'SynHist';
plotInfo(27).Xlabel = 'Distance from soma (\mum)';
plotInfo(27).Ylabel = 'Mean number of synapses';
plotInfo(27).FigName = 'sholl_synapse_analysis';
% "Sholl M"
% n) Synaptic morphology intensity distribution in Sholl analysis: Histogram (as bars, see Fig3D SynD paper)
% y-axis: synaptic morphology intensity (a.u.)
% x-axis: distance from soma (um)
plotInfo(28).Name = sprintf('Synaptic %s intensity distribution in Sholl analysis', ...
morphLabel);
plotInfo(28).Type = 'hist';
plotInfo(28).DataStr = 'IntMorphMean';
plotInfo(28).Xlabel = 'Distance from soma (\mum)';
plotInfo(28).Ylabel = sprintf('Mean synaptic %s intensity (a.u.)',morphLabel);
plotInfo(28).FigName = sprintf('sholl_synaptic_%s_analysis',morphLabel);
% "Sholl S"
% n) Synapse intensity distribution in Sholl analysis: Histogram (as bars, see Fig3D SynD paper)
% y-axis: synapse intensity (a.u.)
% x-axis: distance from soma (um)
plotInfo(29).Name = sprintf('Synaptic %s intensity distribution in Sholl analysis', ...
synLabel);
plotInfo(29).Type = 'hist';
plotInfo(29).DataStr = 'IntSynMean';
plotInfo(29).Xlabel = 'Distance from soma (\mum)';
plotInfo(29).Ylabel = sprintf('Mean synaptic %s intensity (a.u.)',synLabel);
plotInfo(29).FigName = sprintf('sholl_synaptic_%s_analysis',synLabel);
% "Sholl X"
% n) Synaptic X intensity distribution in Sholl analysis: Histogram (as bars, see Fig3D SynD paper)
% y-axis: synaptic X intensity (a.u.)
% x-axis: distance from soma (um)
plotInfo(30).Name = sprintf('Synaptic %s intensity distribution in Sholl analysis', ...
XLabel);
plotInfo(30).Type = 'hist';
plotInfo(30).DataStr = 'IntXMean';
plotInfo(30).Xlabel = 'Distance from soma (\mum)';
plotInfo(30).Ylabel = sprintf('Mean synaptic %s intensity (a.u.)',XLabel);
plotInfo(30).FigName = sprintf('sholl_synaptic_%s_analysis',XLabel);
% "Sholl r(S,M)"
% n) Synaptic synapse/morphology intensity distribution in Sholl analysis: Histogram (as bars, see Fig3C SynD paper)
% y-axis: synaptic synapse/morphology intensity (a.u.)
% x-axis: distance from soma (um)
plotInfo(31).Name = sprintf('Synaptic %s/%s intensity distribution in Sholl analysis', ...
synLabel, morphLabel);
plotInfo(31).Type = 'hist';
plotInfo(31).DataStr = {'IntSynMean', 'IntMorphMean'};
plotInfo(31).Xlabel = 'Distance from soma (\mum)';
plotInfo(31).Ylabel = sprintf('Mean synaptic %s/%s intensity (a.u.)', ...
synLabel, morphLabel);
plotInfo(31).FigName = sprintf('sholl_synaptic_ratio_of_%s_%s_analysis',...
synLabel, morphLabel);
% "Sholl r(X,M)"
% n) Synaptic X/morphology intensity distribution in Sholl analysis: Histogram (as bars, see Fig3D SynD paper)
% y-axis: synaptic X/morphology intensity (a.u.)
% x-axis: distance from soma (um)
plotInfo(32).Name = sprintf('Synaptic %s/%s intensity distribution in Sholl analysis', ...
XLabel, morphLabel);
plotInfo(32).Type = 'hist';
plotInfo(32).DataStr = {'IntXMean', 'IntMorphMean'};
plotInfo(32).Xlabel = 'Distance from soma (\mum)';
plotInfo(32).Ylabel = sprintf('Mean synaptic %s/%s intensity (a.u.)', ...
XLabel, morphLabel);
plotInfo(32).FigName = sprintf('sholl_synaptic_ratio_of_%s_%s_analysis',...
XLabel, morphLabel);
% "Sholl r(X,S)"
% n) Synaptic X/synapse intensity distribution in Sholl analysis: Histogram (as bars, see Fig3D SynD paper)
% y-axis: synaptic X/synapse intensity (a.u.)
% x-axis: distance from soma (um)
plotInfo(33).Name = sprintf('Synaptic %s/%s intensity distribution in Sholl analysis', ...
XLabel, synLabel);
plotInfo(33).Type = 'hist';
plotInfo(33).DataStr = {'IntXMean', 'IntSynMean'};
plotInfo(33).Xlabel = 'Distance from soma (\mum)';
plotInfo(33).Ylabel = sprintf('Mean synaptic %s/%s intensity (a.u.)', ...
XLabel, synLabel);
plotInfo(33).FigName = sprintf('sholl_synaptic_ratio_of_%s_%s_analysis',...
XLabel, synLabel);
% "Profile M"
% n) (Juxta)synaptic morphology intensity profile: Histogram (connected points, basically like you do during extract)
% y-axis: (juxta)synaptic morphology intensity (a.u.)
% x-axis: distance from synapse centre (um)
plotInfo(34).Name = sprintf('(Juxta)synaptic %s intensity profile', ...
morphLabel);
plotInfo(34).Type = 'profile';
plotInfo(34).DataStr = 'meanSynapseProfileMorph';
plotInfo(34).Xlabel = 'Distance from synapse centre (\mum)';
plotInfo(34).Ylabel = sprintf('(Juxta)synaptic %s intensity (a.u.)',morphLabel);
plotInfo(34).FigName = sprintf('juxta_synaptic_%s_profile',morphLabel);
% "Profile S"
% n) (Juxta)synaptic synapse intensity profile: Histogram (connected points, basically like you do during extract)
% y-axis: (juxta)synaptic synapse intensity (a.u.)
% x-axis: distance from synapse centre (um)
plotInfo(35).Name = sprintf('(Juxta)synaptic %s intensity profile', ...
synLabel);
plotInfo(35).Type = 'profile';
plotInfo(35).DataStr = 'meanSynapseProfileSyn';
plotInfo(35).Xlabel = 'Distance from synapse centre (\mum)';
plotInfo(35).Ylabel = sprintf('(Juxta)synaptic %s intensity (a.u.)',synLabel);
plotInfo(35).FigName = sprintf('juxta_synaptic_%s_profile',synLabel);
% "Profile X"
% n) (Juxta)synaptic X intensity profile: Histogram (connected points, basically like you do during extract)
% y-axis: (juxta)synaptic X intensity (a.u.)
% x-axis: distance from synapse centre (um)
plotInfo(36).Name = sprintf('(Juxta)synaptic %s intensity profile', ...
XLabel);
plotInfo(36).Type = 'profile';
plotInfo(36).DataStr = 'meanSynapseProfileX';
plotInfo(36).Xlabel = 'Distance from synapse centre (\mum)';
plotInfo(36).Ylabel = sprintf('(Juxta)synaptic %s intensity (a.u.)',XLabel);
plotInfo(36).FigName = sprintf('juxta_synaptic_%s_profile',XLabel);
% "Profile r(S,M)"
% n) (Juxta)synaptic synapse/morphology intensity profile: Histogram (connected points, basically like you do during extract)
% y-axis: (juxta)synaptic synapse/morphology intensity (a.u.)
% x-axis: distance from synapse centre (um)
plotInfo(37).Name = sprintf('(Juxta)synaptic %s/%s intensity profile', ...
synLabel, morphLabel);
plotInfo(37).Type = 'profile';
plotInfo(37).DataStr = {'meanSynapseProfileSyn', 'meanSynapseProfileMorph'};
plotInfo(37).Xlabel = 'Distance from synapse centre (\mum)';
plotInfo(37).Ylabel = sprintf('(Juxta)synaptic %s/%s intensity (a.u.)', ...
synLabel,morphLabel);
plotInfo(37).FigName = sprintf('juxta_synaptic_ratio_%s_over_%s_profile', ...
synLabel, morphLabel);
% "Profile r(X,M)"
% n) (Juxta)synaptic X/morphology intensity profile: Histogram (connected points, basically like you do during extract)
% y-axis: (juxta)synaptic X/morphology intensity (a.u.)
% x-axis: distance from synapse centre (um)
plotInfo(38).Name = sprintf('(Juxta)synaptic %s/%s intensity profile', ...
XLabel, morphLabel);
plotInfo(38).Type = 'profile';
plotInfo(38).DataStr = {'meanSynapseProfileX', 'meanSynapseProfileMorph'};
plotInfo(38).Xlabel = 'Distance from synapse centre (\mum)';
plotInfo(38).Ylabel = sprintf('(Juxta)synaptic %s/%s intensity (a.u.)', ...
XLabel,morphLabel);
plotInfo(38).FigName = sprintf('juxta_synaptic_ratio_%s_over_%s_profile', ...
XLabel, morphLabel);
% "Profile r(X,S)"
% n) (Juxta)synaptic X/synapse intensity profile: Histogram (connected points, basically like you do during extract)
% y-axis: (juxta)synaptic X/synapse intensity (a.u.)
% x-axis: distance from synapse centre (um)
plotInfo(39).Name = sprintf('(Juxta)synaptic %s/%s intensity profile', ...
XLabel, synLabel);
plotInfo(39).Type = 'profile';
plotInfo(39).DataStr = {'meanSynapseProfileX', 'meanSynapseProfileSyn'};
plotInfo(39).Xlabel = 'Distance from synapse centre (\mum)';
plotInfo(39).Ylabel = sprintf('(Juxta)synaptic %s/%s intensity (a.u.)', ...
XLabel,synLabel);
plotInfo(39).FigName = sprintf('juxta_synaptic_ratio_%s_over_%s_profile', ...
XLabel, synLabel);
plotInfo(40).Name = sprintf('Neurite %s intensity profile', ...
morphLabel);
plotInfo(40).Type = 'gradient';
plotInfo(40).DataStr = 'morphGradientMean';
plotInfo(40).Xlabel = 'Distance from soma (\mum)';
plotInfo(40).Ylabel = sprintf('%s intensity (a.u.)', ...
morphLabel);
plotInfo(40).FigName = sprintf('neurite_%s_gradient', ...
morphLabel);
plotInfo(41).Name = sprintf('Neurite %s intensity profile', ...
synLabel);
plotInfo(41).Type = 'gradient';
plotInfo(41).DataStr = 'synGradientMean';
plotInfo(41).Xlabel = 'Distance from soma (\mum)';
plotInfo(41).Ylabel = sprintf('%s intensity (a.u.)', ...
synLabel);
plotInfo(41).FigName = sprintf('neurite_%s_gradient', ...
synLabel);
plotInfo(42).Name = sprintf('Neurite %s intensity profile', ...
XLabel);
plotInfo(42).Type = 'gradient';
plotInfo(42).DataStr = 'XGradientMean';
plotInfo(42).Xlabel = 'Distance from soma (\mum)';
plotInfo(42).Ylabel = sprintf('%s intensity (a.u.)', ...
XLabel);
plotInfo(42).FigName = sprintf('neurite_%s_gradient', ...
XLabel);
plotInfo(43).Name = sprintf('Neurite %s/%s intensity profile', ...
synLabel, morphLabel);
plotInfo(43).Type = 'gradient';
plotInfo(43).DataStr = {'synGradientMean','morphGradientMean'};
plotInfo(43).Xlabel = 'Distance from soma (\mum)';
plotInfo(43).Ylabel = sprintf('%s/%s intensity (a.u.)', ...
synLabel,morphLabel);
plotInfo(43).FigName = sprintf('neurite_ratio_%s_over_%s_gradient', ...
synLabel,morphLabel);
plotInfo(44).Name = sprintf('Neurite %s/%s intensity profile', ...
XLabel,morphLabel);
plotInfo(44).Type = 'gradient';
plotInfo(44).DataStr = {'XGradientMean','morphGradientMean'};
plotInfo(44).Xlabel = 'Distance from soma (\mum)';
plotInfo(44).Ylabel = sprintf('%s/%s intensity (a.u.)', ...
XLabel,morphLabel);
plotInfo(44).FigName = sprintf('neurite_ratio_%s_over_%s_gradient', ...
XLabel,morphLabel);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
setPlotTypeList();
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function loadData(source, event)
oldDir = pwd;
if(~isempty(loadPath))
try
cd(loadPath);
catch
fprintf('Unable to change to %s\n', loadPath)
end
end
fileType = {'*-save.mat', 'Saved neuron data'; ...
'*.mat', 'Matlab file'; ...
'*', 'All files'};
[dataFile, dataPath, filterIndex] = ...
uigetfile(fileType, ...
'Select neuron image', ...
'MultiSelect', 'on');
loadPath = dataPath;
if(~iscell(dataFile) & dataFile == 0)
% User pressed cancel
return;
end
if(~iscell(dataFile))
dataFile = {dataFile};
end
for i = 1:length(dataFile)
fprintf('Loading %s\n', dataFile{i})
tmp = load(strcat(dataPath,dataFile{i}));
try
tmp.old.neuriteMask;
catch
% Some old format has wrong name.
tmp.old.neuriteMask = tmp.old.neuriteMaskIdx;
tmp.old.somaMask = tmp.old.somaMaskIdx;
tmp.old.neuriteMaskIdx = [];
tmp.old.somaMaskIdx = [];
end
try
tmp.old.somaMeasureMorph;
catch
tmp.old.somaMeasureMorph = [];
end
try
tmp.old.gradientEdges;
catch
tmp.old.gradientEdges = [];
tmp.old.morphGradientMean = [];
tmp.old.morphGradientStd = [];
tmp.old.morphGradientSEM = [];