Segmenting z-stacks for 3D model

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Segmenting z-stacks for 3D model

Fly Guy
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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Re: Segmenting z-stacks for 3D model

Василий Попков
Hi.

You might want to check this article and what (and how) they have done.
http://www.sciencedirect.com/science/article/pii/S2405471217300522

Though, as I know, there is still no easy and established way to do what
you want.

On Mon, Jul 3, 2017 at 1:25 PM, 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
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Vasily A Popkov
Lab.Structure and function of mitochondria
A.N.Belozersky Institute of Physico-Chemical Biology
Moscow State University

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Re: Segmenting z-stacks for 3D model

Jitte Groothuis
In reply to this post by Fly Guy
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
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Segmenting z-stacks for 3D model

Jan Eglinger
In reply to this post by Fly Guy
Hi,

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

There are a few related discussions on the ImageJ forum:

***
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
>
>
>
>
>
>
> ***************************
> With thanks and Best Wishes
> Fly Guy
> Twitter: @flyguy
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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