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Files » MRI_Wound_Healing_Tool.txt

the wound healing macro as a toolset based on the variance in the image - Volker Baecker, 11/16/2011 02:10 PM

 
/**
* Wound Healing Tool
* Collaborators:
* Nathalie Cahuzac, CNRS, IGMM, SPLICOS THERAPEUTICS;
* Virginie Georget, MRI-CRBM
*
* Measure the area of a wound in a cellular tissue on a stack
* of images representing a time-series
*
* (c) 2010-2011, INSERM
* written by Volker Baecker at Montpellier RIO Imaging (www.mri.cnrs.fr)
*
*/


var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Wound_Healing_Tool"
var varianceFilterRadius = 10;
var threshold = 1;
var radiusOpen = 4;
var minSize = 100000;

macro "Unused Tool - C037" { }

macro "MRI Wound Healing Tool Help Action Tool - C000C111C222D07D08D09D0aD0bD0cD0dD0eD0fD18D19D1aD1bD1cD1dD1eD1fD28D29D2cD2dD2eD2fD38D39D3aD3bD3cD3eD3fD40D49D4aD4bD4cD4dD4eD4fD50D51D52D5aD5bD5cD5dD5eD5fD60D61D62D6aD6bD6cD6dD6eD6fD70D71D72D73D7bD7cD7eD7fD80D81D82D83D8cD8dD8eD8fD90D91D93D94D9cD9dD9eD9fDa0Da1Da2Da3Da4DadDaeDafDb0Db1Db2Db3Db4Db5DbeDbfDc0Dc1Dc2Dc4Dc5DcfDd0Dd2Dd4Dd5DdfDe0De2De3De4De5DefDf0Df1Df2Df3Df4Df5Df6C222C333C444C555C666C777C888C999D2aD2bD3dD7dD92Dc3Dd1Dd3De1C999CaaaCbbbCcccCdddCeeeD00D01D02D03D04D05D06D10D11D12D13D14D15D16D17D20D21D22D23D24D25D26D27D30D31D32D33D34D35D36D37D41D42D43D44D45D46D47D48D53D54D55D56D57D58D59D63D64D65D66D67D68D69D74D75D76D77D78D79D7aD84D85D86D87D88D89D8aD8bD95D96D97D98D99D9aD9bDa5Da6Da7Da8Da9DaaDabDacDb6Db7Db8Db9DbaDbbDbcDbdDc6Dc7Dc8Dc9DcaDcbDccDcdDceDd6Dd7Dd8Dd9DdaDdbDdcDddDdeDe6De7De8De9DeaDebDecDedDeeDf7Df8Df9DfaDfbDfcDfdDfeDff"{
run('URL...', 'url='+helpURL);
}

macro 'Measure Wound Healing Action Tool - C000T4b12m' {
setForegroundColor(0, 0, 0);
setBackgroundColor(255, 255, 255);
roiManager("reset")
roiManager("Associate", "true");
run("Variance...", "radius=" + varianceFilterRadius + " stack");
run("8-bit");
setThreshold(0,threshold);
run("Convert to Mask", " black");
resetThreshold();
run("Invert", "stack");
for (i=0; i<radiusOpen; i++) {
run("Dilate", "stack");
}
for (i=0; i<radiusOpen; i++) {
run("Erode", "stack");
}
run("Select All");
run("Enlarge...", "enlarge=-4");
run("Invert", "stack");
run("Analyze Particles...", "size="+minSize+"-Infinity circularity=0.00-1.00 show=Nothing add stack");
run("Clear Results");
roiManager("Measure");
run("Revert");
}

macro 'Measure Wound Healing Action Tool Options' {
Dialog.create("Wound Healing Tool Options");
Dialog.addNumber("variance filter radius", varianceFilterRadius);
Dialog.addNumber("threshold", threshold);
Dialog.addNumber("radius open", radiusOpen);
Dialog.addNumber("min. size", minSize);
Dialog.show();
varianceFilterRadius= Dialog.getNumber();
threshold= Dialog.getNumber();
radiusClose = Dialog.getNumber();
minSize = Dialog.getNumber();
}

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