09.18.13

Eye-Opening Possibilities in Imaging

OpenMSI, a powerful visualization tool developed by Berkeley Lab, may show the way to everything from better biofuels to more effective medicines.

Click to enlarge photo.Enlarge Photo

This overlay of mass spectrometry images shows the spatial distribution of three different kind of lipids across a whole mouse cross-section.Photo courtesy of Wolfgang Reindl (Berkeley Lab)

This overlay of mass spectrometry images shows the spatial distribution of three different kind of lipids across a whole mouse cross-section. Lipids act as the structural components of cell membranes and are responsible for energy storage, among other things.

With the school year just getting underway, teachers are figuring out the learning styles of their students – whether they are obstinate learners (which parents might hear more about at the next parent-teacher conference), linguistic learners who prefer words, or visual learners who prefer pictures and images.

Visuals and images are important in the sciences too. They're especially useful when the original data set looks a bit like the squiggles made from trying to get ink to come out of a pen. And that's what makes OpenMSI, a web-based platform recently established by the Biosciences and Computational Research areas at the Office of Science's Lawrence Berkeley National Laboratory (Berkeley Lab) so important.

The "MSI" part of "OpenMSI" stands for Mass Spectrometry Imaging. Essentially, mass spectrometry is a tool that scientists use to figure out what building blocks – atoms and molecules – something is made of, how those building blocks stack together, and relatively how much of each building block is there. For instance, a researcher might put a droplet through a mass spectrometer and find out that it contains a molecule with the chemical formula C8H10N4O2, and realize that it's caffeine from coffee spilled on the sample.

MSI takes mass spectrometry much further. It transforms the squiggled peaks of those data sets into full-color maps of a sample, with each type of atom or molecule represented by a different shade. Using MSI, scientists can determine the makeup of those molecules, and then visualize how those molecules are spatially distributed. That makes it a powerful tool for everything from developing more effective medicines to creating better biofuels.

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Screen-shot of the OpenMSI online data viewer.Photo courtesy of Oliver Ruebel and Ben Bowen (Berkeley Lab)

Screen-shot of the OpenMSI online data viewer. A mass spectrometry image is shown on the left. Each pixel in this image is literally packed with information. This information is displayed as a complex spectrum (shown on the right) where each peak indicates the presence of a molecule. As researchers click around the image, the spectrum changes to show the molecules packed withing the selected pixel.

However, MSI's data sets are massive, typically ranging from 10-50 gigabytes, the equivalent of some 20,000 digital photos. That makes them clunky to manipulate and challenging to share, both significant obstacles given the collaborative nature of science.

And that's where Berkeley Lab's OpenMSI https://openmsi.nersc.govExternal link comes in. OpenMSI, developed by lead researchers Oliver Ruebel and Ben Bowen, is a gateway that uses the National Energy Research Scientific Computing Center's (NERSC) supercomputing resources to process, analyze, store and serve up MSI data sets to researchers. OpenMSI is web-based, so scientists can simply use their web browsers to study different samples in real-time. The gateway allows researchers to retrieve massive MSI data sets in the blink of an eye (less than .3 seconds to be precise), and its user-friendly interface means that even scientists without programming skills can visualize, analyze and share their data.

OpenMSI already has several detailed data sets up, and more are expected to be added in the coming months. Moreover, there's plenty of power at NERSC on which to draw, including Hopper, a petaflop/s supercomputer capable of performing more than a thousand-trillion operations every second. That means that the possibilities of OpenMSI are just beginning to, well, open.

Learning styles may be different, but what really matters … is the grade. Actually, as teachers will (eventually) admit, what truly matters is not the letter, but rather the lesson; the learning that lives across a lifetime. That's true of efforts at Berkeley Lab, and across the Office of Science as well. OpenMSI is a gateway, and there's every hope that researchers will use it to provide life-long-lasting benefits.

The Department's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information please visit ;http://science.energy.gov/about. For more information about Berkeley Lab, please go to: http://www.lbl.gov/External link.

Charles Rousseaux is a Senior Writer in the Office of Science, Charles.rousseaux@doe.science.gov.

Last modified: 9/18/2013 10:52:06 AM