Posted by
Jeremy Adler on
Mar 24, 2015; 2:59am
URL: http://imagej.273.s1.nabble.com/Manders-coefficient-on-timecourses-tp5012083p5012148.html
The lack of standard test datasets mostly arises because there are many coefficients in play and a test set of images that works for one coefficient may demonstrate the features of another poorly. For example an image intended to maximize the Manders M1 & M2 pair may have almost any correlation.
1) the simplest test is to take any image and use it for both channels. All correlation based methods should then produce a maximum value, usually 1.
2) the other end of the scale take two random images, these can easily be produced in imageJ - here the correlation should be zero, or close to zero. try File\New\Random
intermediate correlations can be generated by using method 1) and adding a random component to each using 2)
________________________________________
From: ImageJ Interest Group [
[hidden email]] on behalf of Cammer, Michael [
[hidden email]]
Sent: 23 March 2015 16:12
To:
[hidden email]
Subject: Re: Manders coefficient on timecourses
Two weeks ago I did a comparison of JACoP with other Pearson's methods (my own, Volocity, and Imaris) and found that JACoP gave different answers for the Pearsons.
I find that people just toss images into these programs without any sort of characterization and often without understanding what colocalization means using different imaging techniques, magnifications, biological conditions, etc.
Are there any standard datasets out there for training people and testing software?
Thanks!
=========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 Temporary location: SK2-7
http://ocs.med.nyu.edu/microscopy &
http://microscopynotes.com/-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Jeremy Adler
Sent: Friday, March 20, 2015 12:24 PM
To:
[hidden email]
Subject: Re: Manders coefficient on timecourses
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");
}
}
--
View this message in context:
http://imagej.1557.x6.nabble.com/Manders-coefficient-on-timecourses-tp5012083.htmlSent from the ImageJ mailing list archive at Nabble.com.
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html