Re: Manders coefficient on timecourses

Posted by jerie on Mar 23, 2015; 3:29pm
URL: http://imagej.273.s1.nabble.com/Manders-coefficient-on-timecourses-tp5012083p5012123.html

On Mon, Mar 23, 2015 at 12:12 PM, Cammer, Michael <
[hidden email]> wrote:
---
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?
---

Michael,

very good topic, my impression is that careless use of coefficients has
made it very tedious to compare results.
For test sets, take a look at http://www.colocalization-benchmark.com/

Jens.

Dr. Jens Rietdorf

Visiting Scientist @ Center for Technological Development in Health (CDTS),
Oswaldo Cruz Foundation (Fiocruz), Ministry of Health, Rio de Janeiro,
Brazil.
http://br.linkedin.com/pub/jens-rietdorf/6/4a3/189/
Skype jens.rietdorf

On Mon, Mar 23, 2015 at 12:12 PM, Cammer, Michael <
[hidden email]> wrote:

> 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");
>         }
>  }
>
>
>
>
> --
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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