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Re: Watershed Question

Posted by Aryeh Weiss on May 24, 2011; 8:32am
URL: http://imagej.273.s1.nabble.com/Watershed-Question-tp3684479p3684480.html

On 5/24/11 10:34 AM, Sebastian Rhode wrote:

> Hi,
>
> I have an 16bit image with some stained cells and wrote I macro which
> automatically detects the cells and converts them into a ROI. First I use
> the RATS (treshold) plugin, which yields in in an 8bit BW image. And to
> separate overlapping cells, I use "Watershed" from the Process/Binary menu.
> This works fine.I end up with well separated ROIs, one for every cells,
> after "Analysis particles".
>
> But when I apply the same workflow to the same data on the PC of my
> colleague, the watershed does not separate overlapping ROIs. There I end up
> with the inverse result. The gaps in between the cells are now the output
> after "Analysis particles", sinve the watershed did not separate the
> regions. Instead they all got connected by lines.
>
> So I think there must be an option concerning the "Watershed", which allows
> me to control this behavior, but I have no idea, where to look for it. any
> idea, what my mistake is?
>
> Cheers,
>
> Sebi
>

Binary-->Options has a checkbox that allow you select black background.
This should solve your problem.

I add that I find the issue of black background vs white background in
ImageJ confusing. For example, the particle analyzer create a mask with
black objects on a white background, but it is actually an inverse LUT,
and really the objects are 255 and the background is zero. Yet sometimes
I run into a plugin that really wants a white background. I have not yet
sorted this out.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051