Are your inputs for both IdentifyPrimaryObjects and IdentifySecondaryObjects binary images? Because if so, and you do not have any intensity information to guide the propagation in IDSecondary, then the boundary can only be specified by the distance between the two touching cells’ nuclei.
But I have two other thoughts:
(1) If you do have raw images with intensity information and not binarized, then IDSecondary should work. I would bring your attention to the “Regularization Factor” in IDSecondary which defaults to 0.05, but adjusting this setting, as the Help says:
But you will note that if there is no intensity info to distinguish the touching cells, as in the binary case, then all you have to go on is the distance from the two nuclei, OR one could use shape information (which is what I assume you are doing by eye to say that the boundaries are incorrect). IDSecondary does not take shape into account, however…
(2) You could also use IdentifyPrimaryObjects directly on the larger, touching cells. Use the declumping settings of Method to distinguish… = “Shape” and Method to raw dividing… = “Shape”. This should draw more veridical boundaries, though if the cells are too close together this may still not work. Then you could use RelateObjects to relate the nuclei and the cells, if needed.