//script parameters
#@ File(label="Directory", style="directory") dir
#@ File(label="Pixel Classification", description="Enter an ilastik project (ilp) file", style="extensions:ilp") project
#@ String(label="Type", choices={"Grid: row-by-row", "Grid: column-by-column", "Grid: snake by rows", "Grid: snake by columns"}, style="radioButtonVertical") type
#@ Integer (label="Tile overlap (%)", value=15) overlap
#@ Integer (label="Mean filter (radius)", value=2) mean
#@ Integer (label="Open (iterations)", value=15) iterOpen
#@ Float (label="Threshold (%)", value=0.35, max=1, min=0, stepSize=0.01, style="slider", persist=false) threshold
#@ 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
threshold/=100;
original=File.getName(dir);
list=getFileList(dir);
Array.sort(list);
outputMerged=File.getParent(dir)+File.separator+original+"_merged";
outputStitched=File.getParent(dir)+File.separator+original+"_stitched";
//check if the folder contains h5 files
h5Files=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");
rename("Final_mask");
//measure
run("Set Measurements...", "area centroid shape redirect=None decimal=2");
selectImage("Final_mask");
run("Set Scale...", "distance="+1/distance+" known=1 pixel=1 unit="+unit);
run("Analyze Particles...", "size=0-Infinity show=Masks display add clear");
roiManager("Save", rawStitchingOutput+File.separator+wellName[i]+"_roi.zip");
roiManager("deselect");
roiManager("delete");
run("Select None");
//store results
areaArray=newArray(nResults);
circArray=newArray(nResults);
arArray=newArray(nResults);
roundArray=newArray(nResults);
solidityArray=newArray(nResults);
xArray=newArray(nResults);
yArray=newArray(nResults);
for (j=0; j