Posted by
Alan Thames on
URL: http://imagej.273.s1.nabble.com/Help-colony-counting-with-image-J-tp5004887p5004914.html
Hi Gabriel, Thanks for the reply.
"> 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."
--->I keep one setting to quantify all.
"
> 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."
I double checked now, without changing any thing, i.e - 8 bit image -
threshold - auto; analyze0 analyze particles --- count was way increased to
thousands (not possible).
"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."
You are absolutely right. The treatment, i believe should decrease both
size and number of the colonies.
I will send a few images to you email, if u hv some time to spare.
Thanks again
Alan
On Sat, Sep 21, 2013 at 6:57 AM, Gabriel Landini <
[hidden email]>wrote:
> 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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http://imagej.nih.gov/ij/list.html>
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