Tuesday, 27 February 2018

Geologists solve fossil mystery by creating 3-D 'virtual tour' through rock


Have you ever wished you could travel inside a rock? It may sound more like magic than science, but Princeton scientists have found a way to make it (almost) true.

Geologists solve fossil mystery by creating 3-D 'virtual tour' through rock
With an industrial grinder, a super-high-resolution camera usually used for wedding photography, and high-speed neural
networks, Princeton geoscientists Adam Maloof and Akshay Mehra can deconstruct rock samples and create three-
dimensional digital versions, which they have used to analyze specimens of Cloudina fossils gathered by Mehra (left)
and undergraduates Will Van Cleve and Christian Gray (right) of the Class of 2017 from the Byng Formation,
a fossil reef formation in a glacier-carved valley on Salient Mountain in the Canadian Rockies
[Credit: Adam Maloof and Akshay Mehra, Princeton University Department of Geosciences]
With an industrial grinder and a super-high-resolution camera, Princeton geoscientists Adam Maloof and Akshay Mehra can deconstruct rock samples and create three-dimensional digital versions that scientists can look at from any angle. In addition, they have developed software that allows the computer to segment images and isolate objects without human bias.

Using this technology in conjunction with detailed field observations, they examined a thin-shelled creature that lived over much of the world about 545 million years ago, Cloudina, generally agreed to be the first-ever "biomineralizer," an organism that can create a shell or bones in addition to soft tissue.

While previous researchers had argued that Cloudina were reef builders, Maloof and Mehra were able to use their 3-D reconstruction of the creatures' delicate tube-like structures to conclude that the fossils had been transported from other areas, suggesting that Cloudina played only a minor role in the earliest reef systems. Their work appears in the current issue of the Proceedings of the National Academy of Sciences.

"I thought going in we would learn all sorts about this amazing first biomineralizer and first reef builder, but Cloudina turned out to be more like a reef dweller," said Maloof, an associate professor of geosciences. He has now turned his focus to the next-oldest potential reef builder, a sponge called Archaeocyathid that lived about 520 million years ago.

Cloudina had proven resistant to detailed study because its delicate casing is too fragile to extract physically from the surrounding limestone, and it could not be imaged remotely with traditional X-ray tomography techniques, which require density differences between the object of interest and the surrounding material. Because Cloudina is chemically identical to limestone, the fossils were effectively invisible to X-rays.

Meet GIRI

Almost five years ago, Maloof a nd Situ Studio collaborator Brad Samuels assembled the technology to create what he now calls "flipbooks," digital renderings that move through more than a thousand wafer-thin slices through a rock. Known as "GIRI" or "the grinder," the Princeton Grinding Imaging and Reconstruction Instrument is an answer to geologists' long-standing desire to know what rocks look like on the inside.

Geologists solve fossil mystery by creating 3-D 'virtual tour' through rock
Princeton University geoscientist Adam Maloof has spent five years perfecting a combination grinder and imaging system
that can create a three-dimensional 'virtual tour' through the inside of any solid object, from rocks to batteries. Here,
a diamond wheel grinds a sample in the Princeton Grinding Imaging and Reconstruction Instrument (GIRI) in the
Grinder Lab behind Guyot Hall, Princeton University [Credit: Adam Maloof and Akshay Mehra,
Princeton University Department of Geosciences]
"Forever -- since Darwin -- people have tried to figure out how fossils look in 3-D, when they're embedded in rock and it's hard to get them out," Maloof said. "People did serial sections just like this way back then -- but perhaps not at this scale -- where they would grind away a little rock, draw it, grind a little more, draw it. ... It can be incredibly time-consuming."

Enter GIRI, which can cut slices as thin as a few microns (less than 1 percent of a millimeter) and can run 24 hours a day for weeks on end. As each slice takes about 90 seconds to cut and image, researchers have to choose between speed and scale. Most of the specimens Maloof and Mehra have imaged are cut into 30-micron slices, about a third the thickness of a human hair. A typical inch-thick, 1,500-slice sample takes about a day and a half to grind and image; during this time, the operator needs to replace machine fluids and clean the wipers (which clear the surface after each cut) only once.

"The process is destructive," Maloof said. "Dinosaur bones, lunar samples -- there are certain specimens that people are less likely to give us. It hasn't really stopped us, because most samples are not precious. Cloudina, there are zillions of them -- we could never grind them all."

GIRI can produce a 3-D rendering of any solid object, whether or not it has the density differences needed for effective X-ray computed microtomography (usually known as X-ray CT or Micro CT). In addition, because you're taking a super-high-resolution photograph with every slice, you're always seeing the rock itself, not just the density model that remote sensing can provide.

"It's destructive of course, that's the disadvantage, but what's so nice is that you get to see photographs and make direct observations," Maloof. "That's what's been so life-changing to me: I love that it's not a model. You can just see it. On any given slice, if you find something great, you can just find the slice and say, 'What did it look like?' ...We're on a virtual tour inside, rather than looking at waveforms and trying to interpret them."

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