Re: Electron microscopy nuclei segmentation

Posted by A A on Nov 28, 2012; 10:46am
URL: http://imagej.273.s1.nabble.com/Electron-microscopy-nuclei-segmentation-tp5000972p5000984.html

Hello Christin,


I'm guessing, with straight forward you mean simple. And from my

> experience, automatic segmentation in TEM pictures of Epon sections is far
> from that. Usually chromatin comes in at least two typical densities that
> again match with other organelles in the cell. I guess you could try the
> trainable segmentation plugin and feed it an image where you select the
> chromatin areas as one class and everything else as background. Train the
> classifier repeatedly and it might become efficient. The problem there is
> that it is time consuming especially on large image formats of several k's
> of pixels (like TEM cameras often produce). So you might want to start with
> cropped images.
>

I used simple thresholding (after smoothing) to detect chromatin patches
and filtered the thresholded objects by size.  This works pretty well for
our data. The problem is that patches belonging to one nucleus are
separate. I need to find a way to assign chromatin patches to their
corresponding nuclei.

Best,
Albina

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