Issues with colocalisation plugins in Fiji

[WHEELER Ann]

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
E: [hidden email]
T: 0131 651 8665
W: http://www.igmm.ac.uk/imaging.htm


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[ctrueden]

Hi Ann,

I was waiting to reply to this thread, to give the Coloc 2 maintainers
first crack at it. Personally I am no colocalization expert and cannot
really comment on the specific technical issues you raise.

However, for the benefit of the interested people in the community, I
wanted to mention the related discussion going on in the Fiji BugZilla
issue tracker:

* http://fiji.sc/bugzilla/show_bug.cgi?id=1100
* http://fiji.sc/bugzilla/show_bug.cgi?id=1082

Bug #1100 in particular raises some social issues surrounding the
development of Coloc 2, as well as ImageJ and Fiji in general, which might
interest some others. However, for those who wish to reply: please do so
here on the mailing list -- the issue tracker should be limited to
discussion of specific technical issues.

> 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.

Please tell us exactly which plugins you mean, and we can add them to the
Fiji distribution.

Regards,
Curtis

On Thu, Jun 18, 2015 at 8:48 AM, WHEELER Ann <[hidden email]>
wrote:

> 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
> E: [hidden email]
> T: 0131 651 8665
> W: http://www.igmm.ac.uk/imaging.htm
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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