wound healing划痕图片批量分析—科研工具箱

修改MRI_Wound_Healing_Tool.ijm细胞划痕插件，实现批处理，相关参数设定参考插件说明http://dev.mri.cnrs.fr/wiki/imagej-macros/Wound_Healing_Tool

将下面代码保存为txt或ijm，imageJ里面Macro–>Plugins–>Macros–>Run–>保存的脚本，然后选择图片所在目录，软件会自动分析。

可能有些图片会有多个结果，原因是细胞过于稀疏或者有空白，也或者划痕区域有杂点等，这种情况下可用插件确认问题，手动进行分析。

软件毕竟不是人脑，程序化操作不可尽信，有疑惑可以double check。

var helpURL = \"http://dev.mri.cnrs.fr/wiki/imagej-macros/Wound_Healing_Tool\"
var varianceFilterRadius = 20;
var threshold = 50;
var radiusOpen = 4;
var minSize = 10000;
var methods = newArray(\"variance\", \"find edges\");
var method = \"variance\";
var measureInPixelUnits = false;

function thresholdVariance() {
    run(\"Variance...\", \"radius=\" + varianceFilterRadius + \" stack\");
    run(\"8-bit\");
    setThreshold(0,threshold);
}

function thresholdFindEdges() {
    run(\"Find Edges\", \"stack\");
    run(\"Invert\", \"stack\");
    setAutoThreshold(\"Percentile dark\");
}

dir=getDirectory(\"Select the source directory\");
list=getFileList(dir);
Array.sort(list);
###修改划痕图片对应格式，此处为jpg，其它对应修改
for(i=0;i<list.length;i++){
	filename=dir+list[i];
	if(endsWith(filename,\"jpg\")){
		open(filename);
	run(\"Select None\");
	getPixelSize(unit, pixelWidth, pixelHeight);
	run(\"Duplicate...\", \"duplicate\");
    setForegroundColor(0, 0, 0);
    setBackgroundColor(255, 255, 255);
    roiManager(\"reset\")
    roiManager(\"Associate\", \"true\");
    if (method==\"variance\") 
        thresholdVariance();
    else 
        thresholdFindEdges();
    run(\"Convert to Mask\", \" black\");
    resetThreshold();
    run(\"Invert\", \"stack\");
    for (j=0; j<radiusOpen; j++) {
        run(\"Dilate\", \"stack\");
    }
    for (j=0; j<radiusOpen; j++) {
        run(\"Erode\", \"stack\");
    }
    run(\"Select All\");
    run(\"Enlarge...\", \"enlarge=-\" + radiusOpen + \" pixel\");
    run(\"Invert\", \"stack\");
    run(\"Analyze Particles...\", \"size=\"+minSize+\"-Infinity circularity=0.00-1.00 show=Nothing add stack\");
    close();
    if (measureInPixelUnits)
    		run(\"Set Scale...\", \"distance=0 known=0 pixel=1 unit=pixel\");
    roiManager(\"Measure\"); 
    roiManager(\"Show None\");
    roiManager(\"Show All\");
    close();
}
}