Coloc2 - quantifying colocalization

Posted by Sylwia J on
URL: http://imagej.273.s1.nabble.com/Coloc2-quantifying-colocalization-tp5008964.html

I am quantifying the colocalization between the green and red channel in my sample (attached) and am not sure if I do it right


I do as follows:

1) Process > Subtract Background (Rolloing ball radius 50 pixels) > OK

2) I draw a shape around a cell

3) Coloc2 > Run (ROI or mask: ROI in channel 1) (PSF 10) (Costes randomisations 10)

My questions are: a) is this correct? in particular the numbers: radius 50, PSF 10, Costes 10 b) in point 3. should I choose the option 'ROI in channel 1' or 'C1-Green'? (these give different values) and c) for Pearson's correlation, do I take the value 'above treshold' or 'no treshold'?

I will be grateful for any comments/suggestions.

Many thanks,

Sylwia