Posted by
Laure Twyffels on
Jan 21, 2016; 10:33am
URL: http://imagej.273.s1.nabble.com/coloc2-plugin-tp5015422.html
Dear all,
I have a few questions about the output of the coloc2 plugin.
1) How are the Ch1 Max threshold and Ch2 Max threshold calculated?
Do they correspond to Costes thresholding?
2) How are the Pearsons below threshold and above threshold R
values calculated? Do they correspond to the values obtained for the pixels
in which at least one channel is below its Max threshold and for the
pixels in which both channels are above their Max thresholds,
respectively? Which use would you make of these values?
3) Is Costes thresholding used for the Manders threshold
coefficients?
And finally, a more general question: I have analyzed only a few images
until now, but for all of them, and all my ROIs, I get a message saying that
The absolute y-intercept of the auto threshold regression line is too
high, and suggesting that I should use a ROI or do a background
subtraction. However, the values of the y-intercept do not seem to me
excessively high (e.g. -1, +3); what I consider as background has a low mean
value too, even inside ROIs. Also, I feel it strange to subtract a
background before asking the plugin to calculate a threshold that is used to
determine what background is. What is your opinion about that?
Thank you for your help !
Laure
Laure Twyffels
Center for Microscopy and Molecular Imaging (CMMI)
Université Libre de Bruxelles
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