Just like you have two eyes that enables you to have stereoscopic vision, you will need two cameras, one for each microscope optical pathway.
Alignment of the two cameras is absolutely critical to achieve viewable 3D. You will need a two video adapters that will be 1) in the same focal plane, 2) be adjustable on the X and Y axis. These will be mounted on side ports on either side of the beamsplitter or light router. Some microscope manufacturers have integrated video adapters that are permanently aligned at the factory.
The other thing is that the CCU for each camera must be genlocked in order for both cameras to be in the same phase. Sony is the only company that has only one CCU for both cameras and does not have to be genlocked.
3D cameras are available in 1080 (2K) and 2160 (4K).