it supposed to take all the .nd files from a folder, do z-projection, set the channel color, adjust brightness and contrast and save them in a new folder as .tiff. However when I run it, it does it just for the first file multiple times
dir1 = getDirectory("Choose Source Directory");
dir2 = getDirectory("Choose Destination Directory");
list = getFileList(dir1);
setBatchMode(true);
for(i =0; i < list.length; i++){
if(endsWith(list[i], ".nd")){
open(dir1+list[i]);
run("Z Project...", "projection=[Max Intensity]");
rename("image");
run("Split Channels");
selectWindow("C1-image");
run("Brightness/Contrast...");
setMinAndMax(106, 200);
run("Blue");
run("RGB Color");
newname=replace(list[i], ".nd", "Blue.tif");
saveAs("Tiff", dir2 + newname);
run("Close");
selectWindow("C2-image");
run("Brightness/Contrast...");
setMinAndMax(105, 320);
run("Red");
run("RGB Color");
newname=replace(list[i],".nd", "Red.tif");
saveAs("Tiff", dir2 + newname);
run("Close");
selectWindow("C3-image");
run("Brightness/Contrast...");
setMinAndMax(102, 300);
run("Green");
run("RGB Color");
newname=replace(list[i],".nd", "Green.tif");
saveAs("Tiff", dir2 + newname);
run("Close");
run("Collect Garbage");
}
}
setBatchMode(false);
print("Finished!")
Try read this link:
https://bioimagerie.univ-rennes1.fr/bioimage/wbarticles/article/3
Dear Gianluigi,
If I see it correctly, you never close the initially opened original image (the Z-Projection creates a copy which is then further processed). This can sometimes lead to weird things happening in batch mode. Have you tried turning batch mode off? Does it work then? Because outside of batch mode, your macro works fine for me. I could not test it with actual .nd files, though, I adapted the code for some .mha images. If the problem was somehow in the .nd-import, you could test for that by using a different file format.
Regards,
Johannes
Hi Gianluigi,
Try using the bioformats plugin to open them. Sometimes Fiji doesn't work well using the standard open(file) if the file isn't a tif. This could certainly be condensed more but it should work as is:
minVals = newArray(106, 105, 102);
maxVals = newArray(200, 320, 300);
colours = newArray("Blue", "Red", "Green");
dir1 = getDirectory("Choose Source Directory");
dir2 = getDirectory("Choose Destination Directory");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i
Try read this link:
https://bioimagerie.univ-rennes1.fr/bioimage/wbarticles/article/3
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