Re: Watershed Question

Posted by Sebastian Rhode-3 on May 24, 2011; 9:07am
URL: http://imagej.273.s1.nabble.com/Watershed-Question-tp3684479p3684482.html

Thanks a lot. Now it works fine. I just added

run("Options...", "iterations=1 count=1 black edm=Overwrite");

to my code and now it works everywhere ...

Sebi

2011/5/24 Aryeh Weiss <[hidden email]>

> 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: [phone]
>
>

--
Dr. Sebastian Rhode
Grünwalder Str. 103a
81547 München
Tel: [phone]
Mobil: [phone]
[hidden email]