Re: help with 3D segmentation

Posted by Gabriel Landini on Nov 01, 2015; 1:40pm
URL: http://imagej.273.s1.nabble.com/help-with-3D-segmentation-tp5014798p5014799.html

On Sunday 01 Nov 2015 15:06:28 Aryeh Weiss wrote:

> I have been asked to do a 3D segmentation of a DAPI stained image, such
> as the image stack available at:
> https://drive.google.com/open?id=0B9hvIdSL8kGyY0NiRzRkaXlINmM
>
> I find that I can do very well in 2D by blurring the image and doing
> peak detection, or gray-scale watershed.
> Gabriel Landini's domes followed by a peak detection or thresholding
> step also works nicely.
> However, I have not succeeded in extending this to 3D, using the 3D
> morphological segmentation tools.
>
> A 3D-domes would be nice, but I have not found that.

Hi Aryeh,
I do not know of a 3D version of the domes, but would applying the domes
algorithm to every slice of the stack do the trick?
Cheers

Gabriel

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