//a pipeline to identify and measure root cell wall intensity

dir1=getDirectory("Get Directory"); 
list=getFileList(dir1);
file="/output/"
prefix="r"
measure = dir1 + file;
File.makeDirectory(measure);

for(i=0;i<list.length;i++){ 
if(startsWith(list[i], prefix)){
 
showProgress(i+1, list.length);
open(dir1+list[i]);

run("Set Scale...", "distance=0");


//duplication image to work on
original_file_name = File.name;
duplicated_file_name = File.nameWithoutExtension; 
run("Duplicate...", "duplicate channels=1 title=&duplicated_file_name");

//processing: there are a lot of conversions but eventhough it's converted to 8-bit, the final measurement is redirected to the 16-bit original image!!!
run("Unsharp Mask...", "radius=5 mask=0.60");
run("8-bit");
run("Auto Local Threshold", "method=Phansalkar radius=15 parameter_1=0 parameter_2=0 white");
//run("Median...", "radius=.5"); //seems like not including this filter gives slightly better results
setOption("BlackBackground", true);

run("Set Measurements...", "area integrated display redirect=[&original_file_name] decimal=2");


run("Analyze Particles...", "size=7-Infinity pixel circularity=0.00-1.00 show=[Overlay] display include in_situ");

saveAs("jpeg", measure+getTitle);
close("*-*");}
}

//setBatchMode("show");

name = File.getName(dir1);
selectWindow("Results"); 
//print(dir1);
//print(name);
saveAs("txt", measure+"Results");