Methods and systems for performing functions with protected data sources from different entities are provided. One system includes a virtual system coupled to an actual system to thereby receive output generated by the actual system for a physical version of the specimen while the specimen is disposed within the actual system. The virtual system includes at least a computer system and a storage medium. The virtual system is not capable of having the physical version of the specimen disposed therein. The virtual system is configured for performing one or more functions for the specimen with two or more protected data sources from two or more different entities, respectively. The virtual system is also configured for performing a virtual version of a process capable of being performed by the actual system for the physical version of the specimen.