help with 3D segmentation

Posted by Aryeh Weiss on Nov 01, 2015; 1:06pm
URL: http://imagej.273.s1.nabble.com/help-with-3D-segmentation-tp5014798.html

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: [phone]


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