To smooth out shaky footage I want to know which of the following apps is the best:
- Final cut Pro X
- Adobe Premiere Pro CS6
- Adobe After Effects CS6
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After Effects, especially with Mocha, has the most advanced motion tracking and stabilization capabilities of these 3 options, but they are also the most complicated to use if you want the best possible results. (Note that AE also does offer simple options like Warp Stabilizer if you don't need super advanced stabilization.)
The options in Final Cut Pro X and Premiere CS6 are far more limited, but both are still reasonably powerful. I will deffer to Guus' answer for that comparison though since I don't have experience working with Final Cut's stabilization.
Definitely the Warp Stabilizer its a very easy to use and powerful tool and I'd say the best tool for automatic stabilization out there. When it comes to the more manual workflow, yes, After Effects together with Mocha is a lot harder to use but you can get very great results with a certain amount of experience. Given that After Effects offers both I definitely go with AJ Henderson's recommendation and always go with After Effects (with optionally Mocha) when it comes to stabilization.