Problem with Auto-Threshold and Watershed

Hi everybody,

I’m looking at particulate matter deposition on various species of vegetation. In line with methodologies from various papers, I am using the auto-threshold plug-in ( The papers also state that they used the watershed feature in order to separate overlapping particles. Unfortunately, when I do this my watershed output (below) comes out with ‘catchment-style’ lines removing the particles altogether. Does anybody know why I might be having this problem?. If I use the standard threshold tool and the watershed function, everything works totally fine but this introduces a degree of human error I would rather avoid. Thanks.

EF_015u_100.tif (1007.9 KB)
EF_015u_100-AT.tif (665.2 KB)
EF_015u_100-AT-WS.tif (665.2 KB)

Hi @GlasgowGI

I do not understand what you want to do.
You want to apply watershed.
Observe both images of the same detail of your image.
Right: watershed
Left: without watershed

Is this type of result you want? So

run("Duplicate...", "title=1");
setAutoThreshold("Li dark");
setOption("BlackBackground", true);
run("Convert to Mask");

Thanks for your help, Mathew. Adding the Convert to Mask step seems to have solved my problem.