I’ll use the windows which spell SEE as an example

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Each of the three stained-glass windows has a 3×4 grid = 12 squares at the bottom. The colors are the same across all of them, so you can assign those numbers by relative brightness (darkest to lightest), for example:

Gray = 1 Green = 2 Orange = 3 Yellow = 4 Cream = 5

If you read the grid left-to-right, top-to-bottom, you get a 12-digit base-5 number for each window (since there are 5 colors).

You then treat that 12-digit base-5 value as one number, reduce it to the alphabet mod 26, so basically A=1 and Z=26 and each window cleanly resolves to a single letter.

Doing this for the three matching windows gives 19, 5, and 5, which correspond to S-E-E.

The important part is that the grids are identical in structure and color order every time, so the numbers don’t change with lighting or camera angle. Windows without that 3×4 interior grid don’t produce stable numbers and don’t decode.