These clues are useful in determining how closely the animals are related to modern species.
In order to find enough fossils to examine, Donoghue's team went back to areas where embryo fossils had been discovered by chance.
"We pull out tons of rock and pick through every little sand grain and decide if it's rock or an embryo," he said.
"On one site, my colleagues picked through 12 [metric] tons [26,000 pounds] of rock and found only 500 embryos."
Donoghue's microscope is at the other end of the size scale.
The instrument uses extremely powerful x-rays generated by a particle accelerator a quarter-mile (four tenths of a kilometer) wide. It functions somewhat like a hospital's CT scanner, but it uses much higher-energy and "purer" x-ray sources.
"It's a fantastic new technology using the word's biggest microscope to look at the word's tiniest fossils," Donoghue said.
Doug Erwin is a paleontologist at the Smithsonian Institution in Washington, D.C. He said the study is "beautiful work and provides an exciting new way of studying some of the most important early animal fossils."
Donoghue's team is already starting to turn its new tool on other types of fossils, including seeds, flowers, and brain cases.
"We're probing the limits of fossilization," he said. "We're seeing features we never thought would be preserved because they're so small."
But the technique also reveals that there's no reason to go to even more powerful imaging methods.
With the new tool, the scientists can see the fossils of individual hairs, but when they try to look inside they find no additional details.
"So we know where the limit is," Donoghue said.
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