NVIDIA Scalable Visualization Solutions Show Theory As Reality at Northwestern University Center for Advanced Molecular Imaging

 
 
An ultra high resolution image of the Helix Nebula from the Hubble Telescope fills the immersive 3D wall at Northwestern University’s Center for Advanced Molecular Imaging (CAMI). (image courtesy of Matt McCrory)
Matt McCrory (L) and Dr. Tom Meade (R) review a protein crystal structure, the work of Northwestern University professor of molecular biosciences and chemistry Dr. Amy Rosenzweig. (image courtesy of Stephen Anzaldi)

Dr. Thomas Meade of Chicago’s prestigious Northwestern University was on a mission. The Professor of Cancer Research, Chemistry, Molecular Biosciences, Neurobiology & Physiology, and Radiology was designing a brand new, state-of-the-art imaging facility with the goal of bringing all biological molecular imaging at Northwestern together under one roof. His Center for Advanced Molecular Imaging (CAMI) aimed to create not only a state-of-the-art tool for researchers, but also a public view of research being done across the university.

“The vision we had was that of a place where everyone from undergrads to professors and researchers could interact with theoretical data in a unique way; to really draw folks in,” said Meade. “We had been thinking about an enormous 2D tiled panel, so that we could look at things very large, like an electronic poster. Then Matt came along.”

Matt McCrory, that is. McCrory is a visualization engineer who had traversed the worlds of science and digital filmmaking, working with Argonne National Laboratory, DreamWorks Animation and the University of Chicago, and was lead visualization engineer for Northwestern University Information Technology (NUIT). He also had a vision for CAMI: stereo 3D; and experience with the technology that could make it work – namely, the NVIDIA® Quadro® Plex, part of the NVIDIA family of Scalable Visualization Solutions.

NVIDIA Quadro Plex systems enable simple and economical installations of ultra-high-resolution, scalable, large-scale visualization environments. The NVIDIA Mosaic™ technology at the heart of the Quadro Plex enables applications to span seamlessly across multiple displays or projectors, reducing the number of workstations needed to power the installation. NVIDIA Quadro Plex and Mosaic multi-display technology both work in stereoscopic 3D as well, enabling researchers to literally immerse themselves into their data.

“With 3D we could translate computational theoretical data that couldn’t be seen any other way,” McCrory said. “It would give researchers a truly holistic view of their subjects. But visualizing high-resolution volumetric data with multiple time steps moves the processing from just three dimensions to four. You need massive amounts of processing power and memory to draw those images quickly enough to make visualization practical.”

McCrory tapped the graphics processing unit (GPU) technology in NVIDIA Quadro Plex to drive the CAMI immersive display – 25 JVC Professional 46-inch stereo 3D displays, stacked five by five, that operate as a single, massive high resolution display on which molecules, proteins, atoms and entire organisms can be displayed in full stereoscopic 3D.

While a typical IMAX theatre displays eight million pixels on a massive screen, the wall at CAMI displays nearly 52 million in a much smaller footprint.

“We wanted to let people get up close and inspect the data pixel by pixel. To drive all of those pixels you need something pretty powerful,” said McCrory. “You need the Quadro Plex.”

13 NVIDIA Quadro Plex multi-GPU systems drive the CAMI display wall -- 26 GPUs in all, with built-in NVIDIA G-Sync II technology to keep all 26 of those GPUs synchronized.

“We basically have a mini-supercomputer driving it,” said McCrory. “I was very familiar with what NVIDIA was doing by adding cores to the GPU, with the stereo capabilities of the Quadro cards, and their support for Linux, which was important for us because we like to run open source. Also, a lot of what we’re doing is volume rendering, and NVIDIA Quadro technology is the best solution to use with those ray-marching algorithms. And you just don’t get the level of video memory that we need on non-Quadro cards.”

On the software side, McCrory developed a GPU-based volume renderer to produce 3D visuals of the facility’s imaging data. The renderer works in conjunction with the open source ImageJ image processing application, which converts CAMI’s imaging data into the layered TIFF format used by the renderer.

“Most of what people see on the display is the output of an interactive application. It’s not pre-rendered but rather interactively drawn on the screen,” he explained. “For a protein crystal structure, for example, it’s just a PDB file converted into a mesh, and this software knows how to render it. For volumetric data like an MRI [magnetic resonance imaging], it’s a Z-stack of images. What this means is that instead of a clinician having to cycle through a series of single grayscale images one at a time, if we write the right tools, people can visualize the MRI in stereo 3D as a continuous surface and see things like lesions more clearly.”

The 3D display wall at CAMI supports visualizations including MRI, whole-body bioluminescence and fluorescence imaging, photon microscopy and scanning probe microscopy of live cells, and allows researchers to visualize data in real time while studying molecular, cellular and tissue structures and interactions.

“There is nothing like standing literally inside your data to truly understand it and get a holistic view of what’s going on,” said Meade.

He relayed the experience of giving a professor her very first look at the crystal structure of enzyme bacteria she had been studying. “Her jaw just dropped and she immediately called her whole lab down to see it. Everyone was stunned. They were blown away by the ability to interrogate the entire structure on a whole new level.” He added, “When I get something new on the 3D wall I don’t even look at the screen any more – I look at people’s faces.”

In addition to students and researchers in Northwestern’s biological molecular imaging areas, CAMI is also open to clinicians from the University’s Feinberg School of Medicine as well as researchers from the greater Chicago area. It can be used to visualize anything that has a 3D data set.

“It’s really one of those things where the sky’s the limit,” said McCrory. “We have astronomers doing incredible work with simulating the evolution of star systems. The Business School has shown an interest in visualizing economic data to show trends. We have requests coming from every school.”

Meade noted, “You need to have a way of visually looking at things versus just looking at numbers. That’s what really gets into our heads.”



 
 
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