http://imagej.273.s1.nabble.com/Colocalization-analysis-using-JACoP-or-Fiji-tp4999119p4999129.html
I'd just like to clarify the point about the Adler and Parmryd publication. They recommend the use of PCC over the Manders overlap coefficient (which is an emasculated version of PCC), not M1 and M2, which are a simple measure of overlap and not controversial. I suggest that PCC should always be used in combination with M1 and M2.
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> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Leonardo Guizzetti
> Sent: 19 June 2012 23:24
> To:
[hidden email]
> Subject: Re: Colocalization analysis using JACoP or Fiji
>
> Hi Aldo,
>
> Perhaps I can help and point you back toward the Coloc2 plugin in
> Fiji/ImageJ. I am doing colocalization of proteins using confocal
> microscopy and turned initialially to the Colocalization plugin within
> ImageJ (using the MacMaster University biophotonics distribution which
> is
> quite stale). Getting into it, the program did not truly handle ROI's,
> and
> as well reported numerically incorrect values for Pearson's. I ended up
> helping debug the Coloc2 plugin (which was also not properly handling
> ROI's).
>
> Long story short, the Fiji Coloc2 plugin does:
> - correctly handle ROI's,binary masks, and full images for all
> parameters
> - Pearson and Mander's coefficients (M1, M2)
> - PSF is only needed for another of the calculated parameters, not
> these
> two in particular.
>
> Right now, the advantage that JaCoP plugin has is a prettier interface.
>
> I will also advise using Pearson's over M1 and M2, as per the
> recommendation of Parmryd & Adler. ( 1. Adler, J., and Parmryd, I.
> (2010)
> Cytometry. Part A : the journal of the International Society for
> Analytical
> Cytology 77, 733-42 [online]
>
http://www.ncbi.nlm.nih.gov/pubmed/20653013. )
>
> Enjoy. :)
>
>
> On Tue, Jun 19, 2012 at 11:56 AM, Aldo Vacaflores <
>
[hidden email]> wrote:
>
> > Hello,
> >
> > I am looking at colocalization of two proteins using TIRF. I would
> like to
> > obtain the Pearson coefficient and M1 & M2 coefficients of only a
> region of
> > interest (ROI) between the two images. Can you select ROI's to obtain
> the
> > different coefficients using JACoP?
> > Also, I tried using Coloc2 which has the option to select an ROI's
> but I
> > can't figure out what value to use when it asks for the PSF. Thanks
> for
> > your help.
> > Aldo
> >
> >
> > --
> > View this message in context:
> >
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> >
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