Posted by
karo03 on
URL: http://imagej.273.s1.nabble.com/Watershed-question-tp3685658p3685662.html
Hi,
As far as I understand, you are not asking for how to call Daniel Sage's plugin but for a solution to separate connected objects. Seemingly you have already tried the way: binarization, distance map (inversion), watershed without sufficiently good results. You try now to apply watershed on the greyscale image, hoping that the resulting bassins contain the expected objects. Am I right? In fact I am convinced that the watershed on grey images will deliver more cumbersome results.
At least a macro line
run("Watershed ", "blurring='1.0' watershed='0 1 0 255 0 1' display='3' ");
from that mentioned demo will work on bright background with dark objects. Hence you have to invert your fluorescence intensity image or change the watershed parameters. Still watershed will typically do more than wished. This falls under oversegmentation, possibly that is what you meant by "it didn't work". This is an inherent problem of watershed. In my applications I change only the amount of blurring or use different methods to smooth the watershed input image (math. morphology or anisotropic diffusion).
Concerning your problem with varying fluorescence intensities, I expect in your images at least a (non-fluorescenting) background which has to be segmented to get objects and/or particles. The necessary threshold should separate background and has not really something to do with varying fluorescence intensities or with the grey values limits in Daniel's watershed algorithm.
I am not sure what you like to do; counting/measuring objects or counting/measuring particles inside of objects. If the objects to be separated are large, watershed on gray images will not be feasible, since grey variation inside the objects delivers further unwished separation.
Perhaps some more information or an example image might be helpful.
Regards
Karsten
Am 11.06.2010 um 21:11 schrieb NatashaW:
> Hi Karsten and Michael,
>
> I need to work with gray level images to get the most of details, so I
> download watershed_.jar plugin from Daniel Sage's website.
> Karsten, Could you please tell me how did you call Daniel's plugin from your
> macro or your java code?
> My problem is that..
> I should use a different threshold value in every time ( I'm working on 40
> images vary in fluorescent intensity) so I need to call watershed algorithm
> from my plugin.
>
> Thank you so much,
> --
> View this message in context:
http://imagej.588099.n2.nabble.com/Watershed-question-tp5168189p5169325.html> Sent from the ImageJ mailing list archive at Nabble.com.
Karsten
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