Posted by
Gabriel Landini on
URL: http://imagej.273.s1.nabble.com/Help-colony-counting-with-image-J-tp5004887p5004891.html
On Saturday 21 Sep 2013 00:24:00 Alan Thames wrote:
> Can any one help me how to get a setting that could count numbers
> proportionate to treatment efficacy and at the same time it would detect
> the decrease in size?
Without knowing anything further, I think that you should not change any
settings to fit your a priory experimental groups.
> If i increase the size setting just
> to count big colonies, the small ones are all missed.
Why? Do not use any size setting, analyze everything there is.
If that leads to false counts, then the segmentation step is incorrect.
> If i decrease the
> size to include all colonies including tiny ones, the count is still
> increased in cells treated with higher drug concentrations, due to the
> presence of tiny smaller colonies, even the big ones are not seen.
You probably need to look at your experimental design from a different
perspective. There might be a relation to treatment in the number of colonies
and their sizes depending on treatment, given that they all need to share the
same plate size. However modifying the quantification step according to
treatment introduces a bias in your sampling that is not scientifically sound:
*you* are introducing a change in the counts.
Cheers
Gabriel
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