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[Orz]

In isometric games, the scenery disappears or fades out when you walk behind it.  It looks like this is usually done by the level designer flagging certain tiles as "roof", "wall", or whatnot.  Anyone have more insight into how this is done in different games?  Is there perhaps an ugly but general solution that doesn't require manual annotation?

[Thaumaturge]

I might suggest having multiple layers of tiles. Then, when the player moves "beneath" a non-empty tile on the "ceiling" layer, one fades out that tile, and any connected to it. (How that connection is handled might depend on the game. If you have only small sections of "ceiling", separated from each other--imagine a village composed of huts--a simple flood-fill, perhaps pre-built, might suffice. If you have large regions of "ceiling"--imagine an expansive dungeon--you might want to have some means of placing tiles into "groups" that can be toggled all together.)

[Orz]

Yeah, on second thought, I won't be able to avoid manual annotation, because the tiles that need to be visible or invisible depend on the scenario.  Right now I just do what you said and organize tiles by hand into groups that fade in or out simultaneously.

Here's a couple references FWIW. 
http://justindjohnson.com/softdev/isometric-occlusion/
This guy uses collision areas to determine occlusion.  AFAIK his underlying data isn't 3D; it's just like a space shooter with funny-shaped buildings.

http://simianzombie.com/posts/2018/01/29/isometric-demo
This guy has a lot more rigorous approach and actually uses a Z-buffer to determine occlusion of moving objects pixel-by-pixel.  He even considers rendering the scene by raycasting into a voxel volume, which sounds rad.

I am keeping it slow & simple: breaking my objects into unit cubes and rendering back-to-front and bottom-to-top.