adjusting watershed in imagej

[Courtney Hart]

Hi everyone,
I'm running a macro that depends on using watershed (using imagej64) to
segment cells that are touching/overlapping in the binary image.  The
problem is that it seems to erroneously be segmenting objects that I don't
want it to.  Is there a way to pass an argument to watershed from the macro
in order to attenuate the effect?  I'm new to imagej macro language, so any
help would be appreciated!

Thanks,

--

Courtney Hart
Research Scientist, Ecovative
[hidden email]
[phone] x1026

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[jerie]

Hi Courtney

>...erroneously be segmenting objects that I don't
want it to.  Is there a way to pass an argument to watershed from the macro
in order to attenuate the effect?

try http://bigwww.epfl.ch/sage/soft/watershed/

Regards, Jens

Dr. Jens Rietdorf

Visiting Scientist @ Center for Technological Development in Health (CDTS),
Oswaldo Cruz Foundation (Fiocruz), Ministry of Health, Rio de Janeiro,
Brazil.
http://br.linkedin.com/pub/jens-rietdorf/6/4a3/189/
Skype jens.rietdorf

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[jerie]

or http://fiji.sc/BioVoxxel_Toolbox#Watershed_Irregular_Structures
or http://fiji.sc/Morphological_Segmentation

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[Michael Schmid]

Hi Courtney,

The ImageJ built-in Watershed can't be adjusted.
Besides the plugins mentioned by Jens, you could also try my Adjustable
Watershed plugin

http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:adjustable_watershed:start

Michael
________________________________________________________________

On Fri, March 27, 2015 17:59, Courtney Hart wrote:

> Hi everyone,
> I'm running a macro that depends on using watershed (using imagej64) to
> segment cells that are touching/overlapping in the binary image.  The
> problem is that it seems to erroneously be segmenting objects that I don't
> want it to.  Is there a way to pass an argument to watershed from the
> macro
> in order to attenuate the effect?  I'm new to imagej macro language, so
> any
> help would be appreciated!
>
> Thanks,
>
> Courtney Hart

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