Fiji - batch processing macro gives inconsistent results - works sometimes

Hi all,

I have been using a small macro to batch process counting particles in images. Each image is a single cell and there’s roughly 400-500 images per condition. The code is below. It worked well initially, it would report the number of particles in images and at the end give me a results. Now it has started to reset during processing, so I end up with only 50-70 results at the end and not the 400-500 I was getting at the start. The results folder does have the correct number of images, but the results table only shows the last 50-70.

I have tried closing Fiji, increasing memory etc, but I just cannot get it to report all the results now, when it did previously.

run(“8-bit”)
run(“Gaussian Blur…”, “sigma=1”);
setThreshold(99, 255);
setOption(“BlackBackground”, true);
run(“Convert to Mask”);
run(“Watershed”);
run(“Analyze Particles…”, “size=2-100 pixel circularity=0.10-1.00 show=Outlines display include summarize”);
run(“Close”);
run(“Close”);

Thank you in advance!