Re: analyze different marked cells

Posted by Guilherme Barbosa on Dec 11, 2014; 4:43pm
URL: http://imagej.273.s1.nabble.com/analyze-different-marked-cells-tp5010893p5010904.html

Hello Jorg

I am not a specialist in programing, but what i would try to do if I were you is:

Try to get a ROI for each cell, using threshold -> analyst particle -> add to ROI, then after that I would split color get the channel that better represents purple and the measure the “amount” of purple in each cell… after it you would have a table on excel with you could determinate the threshold of stain that better represents your cell…. You can double check if the threshold is good, and after it you just ask the excel to count how many cells are under that score.

It looks like a lot of work but you can make it more automatic once you the everything right.

I don’t know if my low experience will help you. But good luck.

Guilherme O. Barbosa.
State University of Campinas
Sao Paulo Brazil

> On Dec 11, 2014, at 1:48 AM, Jörg <[hidden email]> wrote:
>
> Hello everyone,
>
> I try to discriminate between different marked cells (see attached). so i first substracted the background and then did a color threshold. but now i have the problem that there are not only the marked cells i want to count but also some edges of the other cells (2nd attachement). is there any way to get rid of them?
>
> best,
> jörg
>
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