//script parameters
#@ File(label="Directory", style="directory") dir
#@ Integer (label="Mean filter (radius)", value=2) mean
#@ Float (label="Threshold (%)", value=0.35, max=1, min=0, stepSize=0.01, style="slider", persist=false) threshold
#@ Integer (label="Open (iterations)", value=15) iterOpen
#@ String (label=" ", value="![](\"https://live.staticflickr.com/65535/48557333566_d2a51be746_o.png\")
", visibility=MESSAGE, persist=false) logo
#@ String (label=" ", value="Neuromolecular Biology Laboratory
ERI BIOTECMED - Universitat de València (Spain)", visibility=MESSAGE, persist=false) message
// set options
roiManager("reset");
setOption("BlackBackground", false);
setOption("ScaleConversions", true);
setOption("ExpandableArrays", true);
print("\\Clear");
run("Clear Results");
close("*");
// get file list from the Raw Data folder
subfolders=getFileList(dir);
rawDataDir=dir+File.separator+"Raw_Data";
list=getFileList(rawDataDir);
Array.sort(list);
// create a new array containing only the well names without extension
wellList=newArray();
count=0;
for (i=0; i= value[2]=0.9 class[3]=Circ. operator[3]=>= value[3]=0.8 class[4]=-empty- operator[4]=-empty- value[4]=0.0000 combine=[AND (match all)] output=[Keep members] white");
// measure
print("\\Update0:Feature Extraction");
run("Set Measurements...", "area centroid shape redirect=None decimal=2");
run("Analyze Particles...", "size=0-Infinity show=Masks display add clear");
// save rois
print("\\Update0:Saving ROIs");
roiCount=roiManager("count");
for (j=0; j