3D nucleus segmentation

[TimFeinstein]

Hello,

We are trying to count nuclei from confocal XYZ stacks of intact tissue.  This apparently requires a watershed or similar algorithm to separate nuclei that are close to one another.  Ideally it should finish with an annotated image mask to check segmentation quality along with a table of ROI statistics.  I understand that many methods have been implemented in both ImageJ/Fiji and in Vaa3d, but so far we have not found one that works in our hands and provides the desired mask.

If anyone is automatically measuring 3D nuclei in your own work, I would be grateful to hear about your preferred workflow either on or off list.

Many thanks,


Tim

Timothy Feinstein, Ph.D.
University of Pittsburgh Department of Developmental Biology

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[Thomas Boudier-3]

Dear Tim,

I´ve been working on nuclei segmentation for a long time, we have
developed a software specialized for nucleus analysis TANGO :

http://biophysique.mnhn.fr/tango/about

I may also recommend you to have a look to Farsight :

http://www.farsight-toolkit.org/wiki/Main_Page

or work from IJPB :

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start

Hope this helps

Best,

Thomas


On 07/05/15 04:28, Feinstein, Timothy N wrote:

> Hello,
>
> We are trying to count nuclei from confocal XYZ stacks of intact tissue.  This apparently requires a watershed or similar algorithm to separate nuclei that are close to one another.  Ideally it should finish with an annotated image mask to check segmentation quality along with a table of ROI statistics.  I understand that many methods have been implemented in both ImageJ/Fiji and in Vaa3d, but so far we have not found one that works in our hands and provides the desired mask.
>
> If anyone is automatically measuring 3D nuclei in your own work, I would be grateful to hear about your preferred workflow either on or off list.
>
> Many thanks,
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> University of Pittsburgh Department of Developmental Biology
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html