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Unity vs MEF in Prism

Prism offering two injection containers named Unity and MEF. Both the containers have their own capabilities. Before choosing the container decide your environment needs.

Some of the capabilities provided by both (Unity & MEF) containers include the following:
Both register types with the container.
Both register instances with the container.
Both imperatively create instances of registered types.
Both inject instances of registered types into constructors.
Both inject instances of registered types into properties.
Both have declarative attributes for marking types and dependencies that need to be managed.
Both resolve dependencies in an object graph.

Unity provides several capabilities that MEF does not:
Unity resolves concrete types without registration.
Unity resolves open generics.
Unity uses interception to capture calls to objects and add additional functionality to the target object.

MEF provides several capabilities that Unity does not:
MEF discovers assemblies in a directory.
MEF uses XAP file download and assembly discovery.
MEF recomposes properties and collections as new types are discovered.
MEF automatically exports derived types.
MEF is deployed with the .NET Framework.

While choosing which container to use, keep in mind the preceding capabilities and determine which fits your environment/scenario/application/architecture better.

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