So DoomLoader basically ported DOOM to Unity. What I'm doing is running DoomLoader in the background (so it's still a 3D game, technically), but I overlay a UI texture across the screen. I have a script that takes the 3D camera feed, turns it into a render texture (just an array of the pixels that the camera would normally display to the player), applies the algorithm from the paper, and then feeds that to the UI texture as the end display.
The key is that the algorithm needs a depth map. So I made a couple shaders that almost all the objects are now using, which ignore the DOOM textures and instead make all objects greyscale, depending on their distance from the player. So underneath the stereogram, the game is just playing, and every frame looks like a depth map. I'll post an image of that below, with a high "render distance" setting.
The rounding that I've mentioned is in reference to the paper, specifically line 27 if you look at the code in Figure 3 here. The equation is s = round((1-mu*z) * E/(2-mu*z)), which will make more sense if you read the rest.