Posted by
Leonardo Guizzetti on
URL: http://imagej.273.s1.nabble.com/Colocalization-analysis-using-JACoP-or-Fiji-tp4999119p4999123.html
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
>
>
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