Enhancing Anatomical Detail using Computer Colorization Methods

The human eye can differentiate millions of colors, but only about 40 levels of grayscale. So when scientists use biological photomicrographs for teaching or presentation, the monochromatic nature of these images can make it difficult for viewers to discern specific anatomical structures and details.

“For the most part, tissues and cells are quite colorless,” says Dr. Roger Wagner, an electron microscopist and professor emeritus at the University of Delaware. In preparation for microscopy, he says, samples are typically stained to improve visual contrast. But, he explains, this can only help so much—you still have a monochromatic image, and the stain color has little to do with what the specimen looks like in real life to the unaided eye.

As a solution, Dr. Wagner hand-colorizes his digitized photomicrographs using a Macintosh computer and Adobe Photoshop. “I add color in the interest of not only making them beautiful, but to distinguish the different anatomical structures,” he says.

In these three examples of his colorized scanning electron micrographs, Dr. Wagner explains the anatomy using color as reference.

“This is a seminiferous tubule—the location of the development of sperm—which happens to be from a rat. We’re looking at the tubule end-on, and the colors here pertain to different kinds of cells. (Click here to enlarge )

“In spermatogenesis, some undifferentiated cells become differentiated, ultimately to form spermatozoa, which are these yellow structures in the center. So these are the motile germ cells, of course, which fertilize the ovum. Now, there’s a supportive kind of cell in here that simply forms a framework for the rest of the developmental process, and I’ve colored those in green; and they’re called Sertoli cells. They’re a constant resident, and they simply form the framework upon which all this development takes place.

“The blue cells at the periphery are spermatogonia, and these are the totally undifferentiated cells from which all the other cells derive. The purple cells are spermatocytes, an intermediate state of development; and it’s in these spermatocytes that a process called meiosis takes place, the halving of the total number of chromosomes so that the spermatozoa has only a haploid set of chromosomes.”

“I used a little sleight-of-hand here to create this image. It was originally only half of what you see. I duplicated it horizontally and added it to the other half, so it makes it look like a whole specimen. In this image, we’re looking out from in back of the iris, at the anterior surface of the eye. The lens has been removed; the hole in the middle is the pupil. The blue area is the iris, and the peripheral fibers you see are the ciliary fibers and the ciliary muscle, which would be attached to the lens. They result in what we call “accommodation”—the ability to observe things close and far away.

“I’ve colored the iris blue, but it would only look blue from the outside. I’ve colored the ciliary fibers in a greenish shade, with the ciliary muscle here kind of brownish, just so you can see the differences. Now, when this was a grayscale image, I’d have to physically point out all these structures.” (Click here to enlarge )

“What we see here are nerves that are connecting with muscle fibers. These are called “motor end plates” because the signals from these nerves will cause these muscles to contract, and this is where they join. (Click here to enlarge )

What I’ve done here is I’ve colored the nerves a light brown, the muscle fibers in a shade of red, and I’ve also added an artistic filter found in Photoshop called “Plastic Wrap,” which makes the muscle look a little juicy.”

Colorizing Images With Photoshop

Adobe Photoshop includes everything necessary to colorize images, although many additional filters and special effects plug-ins are available through third parties. Dr. Wagner uses his mouse to outline and select portions of each image to be colorized, however some choose to use a drawing tablet and a digital stylus, such as those made by Wacom.

Photoshop often provides more than one way to achieve the same result, and colorization is no different—there are several methods you can follow. The key to success, says Dr. Wagner, is to practice until you get the result you want. “You just have to fiddle with it, and you will know when it’s right,” he says. To learn to colorize images, you can find a selection of free tutorials on the web, and others in books, videos, and at live seminars hosted by organizations such as NAPP (National Association of Photoshop Professionals).

“My colorization is just a personal interpretation,” adds Dr. Wagner. “I try to imagine what things might look like if you were teeny tiny and you could go down and take a peek, and basically that’s where this colorization comes from.

“I just like looking at things. Maybe I’m sort of a frustrated artist masquerading as a scientist.”