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/**
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* Wound Healing Tool
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* Collaborators:
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* Nathalie Cahuzac, CNRS, IGMM, SPLICOS THERAPEUTICS;
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* Virginie Georget, MRI-CRBM
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*
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* Measure the area of a wound in a cellular tissue on a stack
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* of images representing a time-series
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*
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* (c) 2010-2012, INSERM
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* written by Volker Baecker at Montpellier RIO Imaging (www.mri.cnrs.fr)
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*
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*/
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var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Wound_Healing_Tool"
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var varianceFilterRadius = 10;
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var threshold = 50;
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var radiusOpen = 4;
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var minSize = 10000;
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var methods = newArray("variance", "find edges");
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var method = "variance";
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macro "Unused Tool - C037" { }
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macro "MRI Wound Healing Tool Help Action Tool - C000C111C222D07D08D09D0aD0bD0cD0dD0eD0fD18D19D1aD1bD1cD1dD1eD1fD28D29D2cD2dD2eD2fD38D39D3aD3bD3cD3eD3fD40D49D4aD4bD4cD4dD4eD4fD50D51D52D5aD5bD5cD5dD5eD5fD60D61D62D6aD6bD6cD6dD6eD6fD70D71D72D73D7bD7cD7eD7fD80D81D82D83D8cD8dD8eD8fD90D91D93D94D9cD9dD9eD9fDa0Da1Da2Da3Da4DadDaeDafDb0Db1Db2Db3Db4Db5DbeDbfDc0Dc1Dc2Dc4Dc5DcfDd0Dd2Dd4Dd5DdfDe0De2De3De4De5DefDf0Df1Df2Df3Df4Df5Df6C222C333C444C555C666C777C888C999D2aD2bD3dD7dD92Dc3Dd1Dd3De1C999CaaaCbbbCcccCdddCeeeD00D01D02D03D04D05D06D10D11D12D13D14D15D16D17D20D21D22D23D24D25D26D27D30D31D32D33D34D35D36D37D41D42D43D44D45D46D47D48D53D54D55D56D57D58D59D63D64D65D66D67D68D69D74D75D76D77D78D79D7aD84D85D86D87D88D89D8aD8bD95D96D97D98D99D9aD9bDa5Da6Da7Da8Da9DaaDabDacDb6Db7Db8Db9DbaDbbDbcDbdDc6Dc7Dc8Dc9DcaDcbDccDcdDceDd6Dd7Dd8Dd9DdaDdbDdcDddDdeDe6De7De8De9DeaDebDecDedDeeDf7Df8Df9DfaDfbDfcDfdDfeDff"{
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run('URL...', 'url='+helpURL);
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}
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macro 'Measure Wound Healing Action Tool - C000T4b12m' {
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setForegroundColor(0, 0, 0);
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setBackgroundColor(255, 255, 255);
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roiManager("reset")
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roiManager("Associate", "true");
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if (method=="variance")
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thresholdVariance();
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else
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thresholdFindEdges();
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run("Convert to Mask", " black");
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resetThreshold();
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run("Invert", "stack");
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for (i=0; i<radiusOpen; i++) {
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run("Dilate", "stack");
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}
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for (i=0; i<radiusOpen; i++) {
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run("Erode", "stack");
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}
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run("Select All");
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run("Enlarge...", "enlarge=-" + radiusOpen);
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run("Invert", "stack");
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run("Analyze Particles...", "size="+minSize+"-Infinity circularity=0.00-1.00 show=Nothing add stack");
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run("Clear Results");
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roiManager("Measure");
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run("Revert");
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}
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macro 'Measure Wound Healing Action Tool Options' {
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Dialog.create("Wound Healing Tool Options");
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Dialog.addChoice("method", methods, method);
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Dialog.addNumber("variance filter radius", varianceFilterRadius);
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Dialog.addNumber("threshold", threshold);
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Dialog.addNumber("radius open", radiusOpen);
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Dialog.addNumber("min. size", minSize);
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Dialog.show();
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method = Dialog.getChoice();
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varianceFilterRadius= Dialog.getNumber();
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threshold= Dialog.getNumber();
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radiusOpen = Dialog.getNumber();
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minSize = Dialog.getNumber();
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}
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function thresholdVariance() {
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run("Variance...", "radius=" + varianceFilterRadius + " stack");
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run("8-bit");
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setThreshold(0,threshold);
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}
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function thresholdFindEdges() {
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run("Find Edges", "stack");
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run("Invert", "stack");
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setAutoThreshold("Percentile dark");
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}
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