I guessing that these images are artificially coloured, given "nanometer-scale auto fluorescence microscopy" as one of the methods. Quite amazing none the less.
> A high-resolution method, called Airyscan super-resolution microscopy, captured colorful snapshots of organic matter and crystal layers in the kidney stones, “crosscut and truncated” by newer crevices, triangles and other geometrics, Dr. Fouke said.