Re: help with 3D segmentation

Posted by Thomas Boudier-4 on Nov 02, 2015; 2:16am
URL: http://imagej.273.s1.nabble.com/help-with-3D-segmentation-tp5014798p5014807.html

Dear Aryeh,

As mentioned by other colleagues, the seed-based watershed approach
seems the best for your data. The trick here, since the nuclei are here
all  the same size, is to use a 3D BandPass filtering so the nuclei look
more homogeneous. Attached the result I obtained with 3D BandPass
followed by 3D Watershed.

Hope this helps,

Best,

Thomas


On 01/11/2015 21:06, 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.
> I tried peak detection or 2D-domes and then 3D object counting, but
> there is still too much overlap in the Z-direction, so that nuclei which
> overlap vertically are counted as one object.
>
> So I seek to tap into the knowledge available on this list, because I
> am sure someone has already done this type of segmentation.
>
> Thanks in advance
> --aryeh
>

--
   /***************************************************************/
        Thomas Boudier, Associate Professor, UPMC,
        Université Pierre et Marie Curie, Paris, France.
        BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/



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