http://imagej.273.s1.nabble.com/Pls-help-me-with-segmentation-issue-to-count-cell-colonies-in-3D-agars-tp5004983p5004987.html
you can try to use a minimum filter (Process > Filters > Minimum ..).
And maybe there is a chance to improve the imaging. What's your optical
> Dear ImageJ users,
> I have an issue with counting my cell colonies
> in 3D agars. I have attached 8 bit images, in which you can see control image
> has huge and multiple colonies, while the other image treated with a drug,
> 50 uM concentation has multiple tiny
> colonies. When i try to count the colonies number with imageJ, i found
> the count
> " number" is even more increased in treated images, which i do not want
> to see,obviously, though the size of the colonies are counted to be
> decreased with increasing drug concentration ( pls see below results;
> settings - Image>Adjust>Threshold>Auto, Analyze>Analyze Particles, Size: 0
> to infinity, circularity 0-1 and Exclude on Edges) . As one suggested, the
> colonies are all in different planes (ie the agar is too tick to b enabling
> focusing
> in all colonies at once). That will prevent segmenting them right as there are
> too many halo (out of focus) artifacts. Can any one help me with this
> please?
>
>
> Count total Area Average Size
> % area
> Control: 4164 398785.000000 95.769693 12.482002
> 50 uM : 9691 194228.000000 20.042101 6.079352
>
>
> I appreciate it.
>
> Regards,
> Alan
>
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