Thank you for your answers.
If you only need to output to screen, then yes, this is easy with pixel shaders. If you want to save such altered textures, you would need the canvas/image manipulator objects.
In fact, i'd like to be able to import like 3 mask textures packed into a single RGB file, as the memory will handle it as a single texture. I'd use those for operation on the screen like to simulate the shadow of the clouds on the ground or so.
Not sure, what exactly you have in mind.
Here's what I meant :
<img src="http://s2.noelshack.com/uploads/images/18378480478149_whatimeant.jpg">
It can be usefull to avoid creating too small tiles with several variations (using a single really detailed 512 texture instead, which leaves you the possibility to put more stuff in it). Would also it have an impact on performance on huge surfaces (like a dungeon) ?