Re: watershed

Posted by Rasband, Wayne (NIH/NIMH) [E] on Aug 15, 2014; 4:38pm
URL: http://imagej.273.s1.nabble.com/watershed-tp5009231p5009237.html

On Aug 14, 2014, at 11:07 PM, Pamela Young wrote:

> I was giving a FIJI demo yesterday and noticed that
>
> Process>Binary>Watershed
>
> separated joined particles. But if I inverted the LUT, it connects the particles.
>
> I was playing with the Blobs file and just threw a quick threshold on to make a mask.  So the blobs were 255 and the background was 0.  But I didn’t like that the blobs were visually black and the background was visually white.  So I clicked Invert LUT.  The blobs were still 255 and the background was still 0.  But with the new LUT watershed connects all the blobs.  Why does the LUT matter?

Commands in the Process>Binary submenu, such as Watershed,  assume that images contain black objects on a white background. Check "Black background" in the Process>Binary>Options dialog to have them assume that objects are white and background is black. Add

   setOption("BlackBackground", true);

to the Edit>Options>Startup dialog to insure that "Black background" is always enabled when ImageJ starts up (requires ImageJ 1.49e or later).

-wayne
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