Colocalization analysis at the object level
When you are interested in the spatial organization of objects inside a 3D image, measurements like distances to reference objects or to the nearest neighbors can be very useful. But in some biological experiments you may be interested in how different objects overlap, and to what degree they do.
The classical CoLocalization analysis will not help you in this case, as it is focused on coefficients that characterize the overlap of the intensities in the whole image (all VoXels are considered independently of whether they conform an object or not).
The Huygens Object Analyzer contains tools for colocalization analysis between different channels. You can measure the overlap of the segmented objects in terms of volume or intensity, for example. See Object Analyzer Colocalization.
What is an object, anyway? See Object Segmentation.