Imagine a Where's Waldo book with nothing but black and white pictures. Good luck using his candy-stripe sweater as a visual cue. Now you know what it's like trying to find a virus on a greyscale microscopic image. Microbiologists have dealt with this problem for decades, because when things get small, things go dark. Photons, bits of light essential to discerning color, are too clunky to resolve anything much smaller than say, a synapse connecting two neurons. If you want to look at things like viruses, bacteria, or molecules passing through cell walls, you must use an electron microscope.

The devices, developed in the 1930s, use electromagnetic coils to bombard a chemically-prepped, vacuum-sealed specimen with, you guessed it, electrons. The resulting image is more like a shadow casting than a photograph, with the particles revealing shapes, depth, contours, and texture. But not color. Which sucks, because color is an excellent way of finding things—important things—hidden in an image.

Finding all those microscopic Waldos will be much easier, because investigators at the Center for Research in Biological Systems at UC San Diego developed a method for adding color to electron microscopic imagery. The method, published today in Cell Chemical Biology, involves two key technological developments: Treating specimens with rare earth metals, then examining them under a special type of electron microscope typically used to analyze novel synthetic materials.

The colorizing process starts like normal electron microscopy. Electrons like metal, so the microscopist treats the specimen with a heavy metal, like lead, then creates a greyscale image—the base layer. The next step is treating the specimen with different types of rare earth metals called lanthanides (also used in lithium-ion batteries). Lanthanides are pickier than heavy metals and only stick to certain molecule types, which makes those the only molecules the electron microscope sees. The microscopist processes the image, assigns the layer a color—say, green—and layers it on top of the grayscale base layer.

ADAMS ET AL./CELL CHEMICAL BIOLOGY 2016

"So now we have something that makes Waldo stand out from everything else, because we take one picture where everything that wasn’t Waldo disappears into grayscale, and then assign the Waldo molecules a color, like orange, and then put that back together with the greyscale," says Mark Ellisman, microscopist at CRBS and co-author of the study. "We’ve found a way of making multiple Waldos stand out based on the way they interact with the electrons we throw at them." That's fine, but Waldo wore a red (striped) shirt, not orange.

At the moment, the team can add just two or three colors per image. "The hardest part is being able to use several metal treatments in sequence without one cross contaminating the others," says Ellisman. This electron colorizing work builds upon research that earned co-author Roger Tsien, who died in August, a Nobel in 2008. His death has done more than leave the team without a leader. It's left them hurting for money. "We are thinking of crowdfunding to keep his vision going," says Ellisman. The next big goal, in other words, is finding the color green.