You hear Harvard University and think: Smart people there. They ought to know how to preserve great art. So it was baffling and a little tragic when, in the 1960s and '70s, the university allowed the irreversible damage of five murals by the American Abstract Expressionist painter Mark Rothko. Commissioned in 1962 and hung in a student-center dining room, the paintings were faded by sunlight, dinged by furniture, and even marred by graffiti. Finally, under a cloud of shame, Harvard placed the canvases in storage in late 1979. No one knew at the time that a Rothko would someday sell for $87 million, as one did in 2012. But still. The negligence was a travesty.

On Nov. 16 the murals will go back on display at the Harvard Art Museums, in Cambridge, Massachusetts. They will look as if they were freshly painted, but that will be an illusion, because the original colors will appear via light beamed onto the surfaces from ceiling-mounted projectors.

Traditional restoration includes removing surface dirt and varnish, which turns yellow over time, and inpainting, or directly applying paint to bring back faded color and fill in areas where the original material has cracked and fallen away. But it's impossible to revive a Rothko by these methods. For one thing, his paintings don't have a protective varnish, and no ethical conservator would alter a work in a way that could not be reversed. Plus, Rothko made his own paint (and closely guarded the formula) using animal glue, synthetic resins, eggs, and powdered pigments. The unique recipe gave him one of his desired effects: saturation to the point that the color actually penetrated the canvas, creating visual depth.

Panel One, Panel Two, and Panel Three, 1965.

The current restoration effort effectively began with Kodak Ektachrome color transparencies of the murals, taken in 1964. The transparencies themselves were faded, so conservation scientists from Harvard worked with experts from the University of Basel to digitally restore the original colors. Rothko's son, Christopher, then provided the crucial piece of reference: a sixth mural that his father had painted for the installation but stashed away. "It had seen the light of day for only a couple of hours," he says. "They had the original colors and could know with quite some certainty that they were accurate."

Using the Ektachromes and the sixth mural as references, MIT's Ramesh Raskar, a pioneer in computational photography, coded an algorithm that allowed him to fine-tune the color, pixel by pixel, so that the projections compensated for fading and damage rather than simply covering it up. The painting and the light work in concert to create the image of the mural as new.

Christopher Rothko wonders whether the restoration method might draw criticism as painting by numbers, albeit with light. "There's tremendous potential for something good to come out of this, but also tremendous potential for controversy," he says. "This is the bioethics piece of the art conservation world. I'm interested to see how it plays out. My father's work is kind of the guinea pig for this process. I hope it's not something that is just looked at and put away in a closet." Again.

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