Re: count nuclei in low mag image

Posted by Adam Hughes on Nov 22, 2013; 2:50am
URL: http://imagej.273.s1.nabble.com/count-nuclei-in-low-mag-image-tp5005647p5005648.html

You might want to try an adaptive threshold.  Not 100% how to do it in
imageJ actually, but here's an example:

http://scikit-image.org/docs/dev/auto_examples/plot_threshold_adaptive.html

I'd expect this would clean up the contrast differences which are causing
the larger images to be over-adjusted.


On Thu, Nov 21, 2013 at 9:16 PM, katrina <[hidden email]> wrote:

> <http://imagej.1557.x6.nabble.com/file/n5005647/Cocx_1_2.gif>
> Hello all,
>
> I am trying to count the number of cells (white dots) and detect the x,y
> coordinates of each one in this image.  I've tried using Fiji to do this
> but
> I can't detect all of the individual cells very well.  This is what I've
> tried:
>
> 1. Process>>Filter>>Gaussian Blur to run a Gaussian Blur Filter (I've also
> tried without running this filter)
> 2. Image>>Adjust>>Threshold>>Select Dark Background to separate the cells
> from the background
> 3. Process>>Binary>>Watershed to try to separate touching cells, but it
> doesn't separate larger clumps of cells very well as shown below.
> <http://imagej.1557.x6.nabble.com/file/n5005647/Cocx_1_2_segmented.gif>
>
> Can I do any additional processing so that I can identify individual cells
> better?  I don't need to preserve the size of the cells, just their
> position
> and the total number of cells.
>
> I would greatly appreciate help with this!!!!  Thank you!
>
> Katrina
>
>
>
>
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