//clean up print("\\Clear"); if (isOpen("ROI Manager")) { selectWindow("ROI Manager"); run("Close"); } if (isOpen("ResultsTable")) { selectWindow("ResultsTable"); run("Close"); } run("Close All"); //setOptions setOption("BlackBackground", false); //disables the Process>Binary>Options "Black background" option setOption("ExpandableArrays", true); //some variables objectTag="_Object Predictions.tiff"; probabilitiesTag="_Probabilities.h5"; roiInTag="_RoiSet_IN.zip"; roiOutTag="_RoiSet_OUT.zip"; roiAxonTag="_RoiSet_AXON.zip"; //get directory and file list dir=getDirectory("Choose a Directory"); list=getFileList(dir); //count tifs images=newArray; count=0; for (i=0; i1) { options=newArray(particles); for (k=0; k0) { run("Wand Tool...", "tolerance=0 mode=Legacy"); selectImage("OuterMyelin_CountMasks"); doWand(xIn[j], yIn[j]); run("Create Mask"); rename("outline_mask"); run("Set Measurements...", " area redirect=None decimal=2"); run("Analyze Particles...", "display add"); areaOut[j]=getResult("Area", 0); run("Clear Results"); close("outline_mask"); roiCount=roiManager("count"); roiManager("select", roiCount-1); roiManager("rename", roiNumberIn[j]); } else { areaAxon[j]=NaN; areaIn[j]=NaN; areaOut[j]=NaN; } } roiManager("Save", dir+name+roiOutTag); roiManager("deselect"); roiManager("delete"); run("Select None"); close("OuterMyelin_CountMasks"); //measure axoplasm for (j=0; j1) { options=newArray(particles); for (k=0; k