Posted by
Aryeh Weiss on
Nov 01, 2015; 2:17pm
URL: http://imagej.273.s1.nabble.com/help-with-3D-segmentation-tp5014798p5014803.html
On 01/11/2015 3:47 PM, Gabriel Landini wrote:
> 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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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
Hi Gabriel
Thank you for your quick reply. I tried this with the stack version of
your domes plugin.
I still have the problem of how to separate the objects in Z.
Never the less, that is an approach I am looking into.
It seems to me that the 3D-watershed plugins should work, but I have not
found the right parameters.
Best regards
--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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