Posted by
Jeremy Adler on
Mar 20, 2015; 4:23pm
URL: http://imagej.273.s1.nabble.com/Manders-coefficient-on-timecourses-tp5012083p5012098.html
A general request, when refering to Mander's coefficients it would be useful to make it clear which coefficients are being considered - an annoying feature of many papers.
The 1993 paper refers to M1 & M2, the Overlap coefficient and k1 & k2 - all could be called Mander's coefficients.
Referring to Mander's overlap coefficients is no better as this could cover M1 & M2 which cover the overlapping fraction each fluorophore and the Overlap coefficient.
M1 & M2 are clear and useful, the Overlap coefficient is far less useful than the Pearson correlation coeff (also features in the 1993 paper) while k1 & k2 derive from the Overlap coefficient and it is unclear, to me, what they really indicate.
________________________________________
From: ImageJ Interest Group [
[hidden email]] on behalf of Cath Heyward [
[hidden email]]
Sent: 20 March 2015 16:01
To:
[hidden email]
Subject: Manders coefficient on timecourses
Hi all,
I'm looking for a way to measure Manders coefficients between two channels
over time. So far I found a couple of plug-ins to measure Manders
coefficients that work on stacks (e.g. JaCoP, Manders coefficients_class),
but these seem to pool all the values into one instead of returning the
individual values for each slice as I would need for a time course.
Is there a plug-in I haven't found that will do this for me?
I also tried writing a macro to use the plug-in on each slice individually
(see below for code) but I get the same values for all the slices, so I
assume this is still pooling together all the slices. I tried ticking the
"Use current slice only" box but the macro recorder gives an error for the
keyword "use" being used three times so I don't think the "use current slice
only" command is being obeyed. Can anyone offer any suggestions for how to
get round this?
Thanks in advance,
Cath
macro "Measure Manders Stack" {
frames=nSlices;
run("Clear Results");
for(i=0; i<frames; i++) {
currentslice=i+1;
setSlice(currentslice);
run("Manders Coefficients", "red=redtest.tif green=greentest.tif
channel=[Red : Green] use=None use use exclude");
}
}
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