Colocalisation

Posted by Paul Buchanan on Sep 19, 2013; 2:20pm
URL: http://imagej.273.s1.nabble.com/Colocalisation-tp5004854.html

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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