> 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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