How to measure colocalization?


Hello, I have stacks of images that I want to check for colocalization. What would be a possible way to do that in CellProfiler?
1 - how do I arrange the stacks, so that the right pictures are pairwise together?
2 - which module do I use for colocalization detection?

Sorry for posting so many (trivial) questions, but I just started using the program.
Thank you for your patience,

Keep up the good work, Daniela


Hi Daniela,

  1. Typically, a single LoadImages module is all that is needed to load in multiple associated images (e.g. different wavelengths of the same sample). However, from your other posts, your situation is a bit different (stacks of images in .stk format). Although I think we have addressed those issues already, no?

  2. Use the Relate module for colocalization, once both sets of objects have been segmented with (usually) IdentifyPrimAutomatic.



You might also find the MeasureCorrelation module to be helpful to measure the correlation (a.k.a. colocalization) between the intensity signals in two channels. David’s response is for when you have objects in two channels that you want to relate to each other. If instead you want to know how much two wavelengths (i.e., channels) colocalize, the MeasureCorrelation module will be more suitable. You can measure the colocalization across the entire field of view, or instead you can identify objects (e.g., nuclei or cells, using an Identify module) and then measure the correlation within each object or subcompartment you have defined.