http://imagej.273.s1.nabble.com/help-with-3D-segmentation-tp5014798p5014802.html
Works with difference of gaussian to find peaks, in nd (the example is in 3D just like in your data).
The key in DoG is to determine the two sigmas. A bit of experimentation will take you there.
> On Nov 1, 2015, at 8:06 AM, Aryeh Weiss <
[hidden email]> 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
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph: 972-3-5317638
> FAX: 972-3-7384051
>
>
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