Interactive Marker-controlled watershed. MorphoLibJ

Hi! I was trying the Interactive marker-controller watershed plugin. Is there any way to adjust the watershed parameters to control the flooding and obtain a better segmentation result? Having the gradient image (very clear borders and background) is not helping :frowning:

And also, I am unable to obtain any segmentation result from ROIs saved in the Roi manager window, which is a real pity! I am using Fiji and last version of MorphoLibJ.

Any help would be really appreciated.

Thanks a lot,


HI Veronica,

First, what do you mena by “better result” ?
The principle of marker-controlled watershed is to manually specifiy markers. Therefore, you should have as many regions as the number of markers you specify.
The boundaries of the regions may be adapted by smoothing the input image before computing the watershed.

Maybe you can provide an example image?


1 Like

Hi David. Thanks for you comments. Yes, it was definitely the number of markers, I added several more and now it really segments quite good. Regarding the RoiManager question… if rois are not point selections then they must be combined. Everything works really fine. Thank you again.