Posted by
WHEELER Ann on
Jun 18, 2015; 1:48pm
URL: http://imagej.273.s1.nabble.com/Issues-with-colocalisation-plugins-in-Fiji-tp5013203.html
Dear Listers (or perhaps more specifically people who write the colocalisation plugins).
We are having a couple of issues with the newly implemented colocalisation plugins in Fiji. The output from Coloc2 isn't as good, shall I say than it's predecessors.
What we want to do is set thresholds ourselves for 2 stainings and see if, at the threshold level we set, they colocalise in specific ROIs.
I want to look at Manders coefficients M1 and M2, Percentage overlap CH1:Ch2 and vice versa for area and intensity. I would like the ability to pick which data I see rather than having a lot of numbers which I don't need to sift through. I then want an output file which details in tabulated form:
Slice Region Threshold Ch1 Threshold Ch2 M1 M2 %overlapCh1 %overlapCh2
1 1
1 2
1 3
2 1
2 2
2 3
At the moment the output is a rather horribly long list which is not user friendly
In the colocalisation threshold plugin scatter plot graph the axis aren't labelled. I have no idea if the x axis is Channel 1 and the y axis is channel 2 or what. I reckon this would be a pretty simple bug for someone who knew how to program java (i.e. not me) to fix.
This should all be easy to put into a script so we can batch process and at the moment the script doesn't work at all (partly to do with the horrible output)
I think this is really a matter for the people who write the colocalisation plugins as the functionality I describe was available in the IJ1 plugins and ideally would be reimplemented.
Thanks
Ann
Dr Ann Wheeler
Advanced Imaging Resource, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU
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