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"The game I play is a very interesting one. It's imagination in a tight straightjacket, which is this: that it has to agree with the known laws of physics. [...] It requires imagination to think of what's possible, and then it requires an analysis back, checking to see whether it fits, it's allowed, according to what's known, okay?"
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February 09 2012
Rapid Visual Inventory & Comparison of Complex 3D Structures
Graham Johnson, TSRI & grahamj.com; Andrew Noske, NCMIR; Bradley Marsh, IMB
In this video, Ph.D. animator Graham Johnson of the Scripps Research Institute in San Diego, California, and colleagues take the normally jumbled pieces of a mouse pancreatic cell and stack them into neat piles. It's an organizational feat sure to please cleanliness-loving scientists. But the visualization also gives researchers and students a new look at the abundances and relative sizes of organelles, from mitochondria to insulin granules. “The cell is a lot more complicated-looking than most people think of it,” Johnson says. “We wanted to clarify it.”
The video opens with a 3D model of a chaotic cell taken from the pancreas as seen in its natural state. Thousands of irregularly shaped organelles huddle around a central and bean-shaped nucleus. Then, Johnson and colleagues start to spring-clean. Drawing on data from the lab of team member Bradley Marsh, a cell biologist at the University of Queensland in Brisbane, Australia, the researchers simplify the cell's components and then sort them by organelle. They first group together the mitochondria (green) and insulin granules (blue), then clump these and other organelles together to form uniform columns and rows for easy comparison.
The resulting image looks less like a cell and more like a 3D abacus. But it also displays the relative volumes of these cellular factories and compartments. Surprisingly, for instance, mitochondria occupy only 7% of the cell volume, which is hard to see from the raw cell alone.
This visualization, Johnson says, represents the middle ground between the two standard depictions of the cell: the natural, or chaotic, cell and the cartoonish, or textbook, cell. That became clear when the team showed the video to school kids in Australia: “When they could see the random, video-game-looking cell morph into the type of cell that their teacher had been presenting to them from textbooks and the Internet,” he says, “they really got excited.”
The team “manages to weave into one short video an unbelievable amount of information,” says challenge judge Tierney Thys. “From morphology to volumetrics and beyond, it presents completely different data sets in a seamless, accessible, and aesthetic manner.”
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