Posted by
sonia fargue on
Sep 19, 2013; 3:10pm
URL: http://imagej.273.s1.nabble.com/Colocalisation-tp5004854p5004855.html
Hi Paul,
I will not comment on principles of colocalisation, as I not competent
enough and there better people to answer that.
I just wanted to point out that one reason you may find the JACoP so slow
is that you may be running too many analyses in it. I have found that by
selecting which parameters I really needed, there was little difference
between the two.
Depending on your data, the JACoP also offers the possibility to adjust the
thresholds manually, which in some situations may be more important (if
matching intensities in the pixels where correlation is analysed are not of
primary interest, but objects are).
Again, there are lots of knowledgeable people in the community.
For a good overview of colocalisation analysis principles, I found the
review by Bolte and Cordelière (J Microscopy 2006) most helpful. You may
already have read it, in which case good luck!
regards
Sonia Fargue
2013/9/19 Paul Buchanan <
[hidden email]>
> Hi All,
>
> Hoping you can give me a few pointers with regards to co-localisation in
> image j and FiJi.
>
> Firstly can some one explain to me in a bit more about intensity based
> co-localisation. To generate a histogram from which the correlation
> co-efficient can be generated, the intensity of one can is plotted against
> the other. But how does this take into account the location of the pixels?
> Sure this method just tells you if pixels in one channel have a similar
> intensity to another channel? How does that describe co-localisation. I
> have read all the papers referenced for the plug ins but just missing out
> on a few basic principles.
>
> I have been using coloc2 and JaCop to look at receptor co-localisation
> with various endsomes as it traffics through the cell. Firstly i have been
> finding JaCoP extremely slow, so slow i cant run it with my images. Ok my
> images are ~200mb each and have about 20 slices in each but coloc2 runs
> through in about 5 - 10 minutes. I have been getting some r values and they
> seem to represent what i see in the overlay images with regards to more or
> less yellow colour. But i have been asked when explaining my work what
> exactly the Pearsons coefficient shows and as stated above am unsure if it
> represents location of co-localisation as well as the intensity. Also am
> not sure if this r value represents the whole z stack i have imaged? and
> what what about slices that have no co-localisation due to being above or
> below the cell does this on skew the results.
>
> I have been looking into doing some object based colocalisation as it
> seems like it would be a better method to confirm co localisation over my z
> stacks but again jacop takes ages to do anything.
>
> Any advice would be gratefully appreciated.
>
> Thanks
>
> Paul Buchanan
>
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