Re: Colocalisation

Posted by Michael Schell-2 on Sep 19, 2013; 5:07pm
URL: http://imagej.273.s1.nabble.com/Colocalisation-tp5004854p5004861.html

> Also with JaCoP the thresholding tab, i dont need to change any of the settings, as it should do it automatically is that correct?
>

In theory, using  auto-threshold is a good thing because it avoids bias and/or error introduced by manual thresholding.  In practice, I find that the auto-threshold in JaCoP (Costes') sets the value too low compared to what my eye thinks is biologically relevant.   For a non-nuclear organelle, using cells stained with antibodies that produce low background, I tend to set the manual threshold to the first value above when all pixels in the nuciei are below threshold.  This value is always higher than the Costes' auto-threshold.  The biological question being tested should be considered when when sets a manual threshold.

Michael
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