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Re: Segmenting z-stacks for 3D model

Posted by Jan Eglinger on Jul 05, 2017; 11:10am
URL: http://imagej.273.s1.nabble.com/Segmenting-z-stacks-for-3D-model-tp5019024p5019030.html

Hi,

I recommend KNIME [1] to easily 3D-segment and count/measure objects.

There are a few related discussions on the ImageJ forum:

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http://forum.imagej.net/t/segmentation-counting-cells-in-3d/2279?u=imagejan

http://forum.imagej.net/t/knime-image-processing/91?u=imagejan

http://forum.imagej.net/t/identify-nuclei-and-spots-in-imagej/94?u=imagejan
***

Also have a look at the example workflows accessible from the Example
Server within a KNIME installation.


Cheers
Jan



[1]: http://knime.imagej.net/

On 03.07.2017 12:25, Fly Guy wrote:

> Hello ImageJers’
>
> I have a set of z-stacks of adult Drosophila brains where some of the cells (neural stem cells and neurons) are GFP-positive.
> There is also a bit of GFP+ background.
> I want to segment and reconstruct a 3D model of the GFP+ cells only (obviously without the background). Then I want to count the cells and measure their volume.
> After fiddling around with binary masks, 3D ROI and 3D segmentation, I am still at a loss for a ‘standardised’ way.
>
> Can someone kindly suggest a plugin etc or a methodology to solve the problem?
>
> Thanks and Best
> FlyGuy
>
>
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>
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>
> ***************************
> With thanks and Best Wishes
> Fly Guy
> Twitter: @flyguy
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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