Re: Segmenting z-stacks for 3D model

Posted by Jitte Groothuis on Jul 04, 2017; 8:32am
URL: http://imagej.273.s1.nabble.com/Segmenting-z-stacks-for-3D-model-tp5019024p5019029.html

Hi FlyGuy,

A seemingly straightforward task, but it can be quite cumbersome...
I would suggest using the TrakEM2 plugin (included in FIJI). You can
segment individual cells in separate AreaLists and get measurements
afterwards. Perhaps the Segmentation Editor could also work.

Good luck,
Jitte

On Mon, 3 Jul 2017 at 12:25 Fly Guy <[hidden email]> 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
>
>
>
>
>
>
> ***************************
> With thanks and Best Wishes
> Fly Guy
> Twitter: @flyguy
>
>
>
>
>
>
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