This solution contains samples when using Windows Authentication.
This sample shows how to use Windows Authentication when hosting your IdentityServer behind IIS (or IIS Express). The salient piece to understand is a new LoginWithWindows action method in the AccountController from the quickstarts. Windows authentication is triggered, and once the result is determined the main authentication session cookie is created based on the WindowsIdentity results. Also, note there is some configuration in Startup with a call to Configure<IISOptions> (mainly to set AutomaticAuthentication to false).