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Can you please share a little more detail around what you wish to monitor specifically?
For the .NET agent, we have a variety of ways to capture information that may not be captured out of the box, such as defining a custom POCO entry point, for example. Please see docs for more information:
If that doesn't do the trick, we have a good amount of community extensions available to pull in metrics you wouldn't otherwise get with an out of the box agent:
If you do not see an extension available to meet your needs, you can always build your own extension!
The link above explains extensions more in depth. Please note that all extensions are FREE and do not consume licensing, assuming you are already a paid AppDynamics customer. Also note that you must have a Machine Agent running in your environment as a prerequisite to installing an extension.