For this trophy, the map is your friend as it helps highlight areas you've visited, so by default, those you've not. The part under the grind rail that you see on the map in a secret area that the magneboots take you too. There are no brains in there. There's also an underground section when you're one the platforms. Each big floaty brain with tentacles rewards you with 3 brains. There are a total of 90.
Jetpack mission 10
Infobot mission 20
Final 'box breaker' mission 60.
Bear in mind, this trophy doesn't pop until you've returned to the brain scientist and handed them in.