Country Scientist — Doing Science With a Digital Scanner

Country Scientist — Doing Science With a Digital Scanner
This living dragonfly was scanned by placing it inside an opening cut in a sheet of corrugated board.

The transition from film to digital cameras has made a huge impact on how amateur scientists can save, analyze, catalog, and publish their imagery. It’s safe to say that digital cameras and personal computers are among the most important tools in the amateur scientist’s kit.

When the subject is two-dimensional, flatbed digital scanners can also play a major role in imaging science. They are ideal for making high-resolution images of leaves, dragonflies, butterflies, tree ring sections, soil samples, and many other subjects.

Advantages and Disadvantages of Scanning

Virtually shadow-free lighting is a key advantage of a digital scanner, for the scanner provides its own light source. Another advantage is that scanners don’t suffer from the distortions caused by camera lenses. Scanners are relatively inexpensive, and they can be used for many applications beyond the scientific roles described here.

Besides their two-dimension limitation, a major drawback of scanners is that objects being scanned must fit within the scanner’s image plane. Scanners are also much larger than digital cameras.

Background Color

Most objects that I’ve scanned looked best with a white background. Because my scanner (HP Scanjet 3970) has a 35mm slide scanner slot built into its lid, it’s necessary to cover the object being scanned with an uninterrupted background. Two or three sheets of white 20-pound paper work well.

Light-colored objects are not easily visible when scanned against the white background of a typical scanner lid. To provide contrast with light-colored objects, place black construction paper over the object being scanned before closing the lid. You can use various colors for special effects.

How to Scan Dragonflies

For years I have photographed dragonflies and damselflies by quietly sneaking behind them. With practice, it’s possible to get within a few inches of some species. While real-world images like these are important, entomologists Forrest Mitchell and James L. Lasswell of the Texas AgriLife Research and Extension Center at Stephenville, Texas, have used digital scanning to create an impressive library of top and side views of many dragonflies and damselflies.

The images at Digital Dragonflies were made by cooling each specimen in a refrigerator to keep it still while it was being scanned. The insects were then placed backside down on the scanner’s glass bed. They were protected from being crushed by the scanner’s lid by placing them inside a 10cm×12cm rectangle cut in a mouse pad (see their website for details). The mouse pad approach is probably best, but I’ve found that ordinary corrugated fiberboard will also work.

Based on my experience scanning dragonflies, it would seem that butterflies and moths could also be scanned. A severe drought has slashed the butterfly population in Central Texas, and I’ll try this method as soon as the butterflies return.

Fossils and Artifacts

Fossils and artifacts having a flat surface are easily scanned. For example, I’ve scanned the fossil of a trilobite with good results. Even ripple marks in the mud (now shale) on which the creature was resting were captured.

Years ago I found a flint artifact in the gravel bottom of the creek that borders our land. The artifact is a flint scraper that is very flat on both sides, and it was easily scanned against a white background. Flint arrowheads and spear points can also be scanned.


The leaves of many kinds of plants are easily scanned against a white background.

The main limitation of scanning leaves is the size restriction posed by the scanner’s bed.

For best results, scan plant samples as soon as possible after collecting them. If this isn’t possible, preserve the sample in a cool location or immerse its stem in water. Leaves may be coated with wax, so be sure to clean the scanner’s glass bed after scanning.

The color of scanned leaves may not appear true to life. If not, you can use a photo processing program to correct the color. I’ve found that the best way to accomplish this is to hold the actual sample next to the monitor and adjust the color of the image until it matches that of the sample.


Most flight and tail feathers are easily scanned, but white feathers and those with white down require a dark background. For example, I once scanned a flamingo feather. The upper half of the feather was pink, and it scanned fine. Because the lower portion of the feather was white, it was barely visible against the white background. The entire feather was visible when a sheet of black paper was placed over it.

Soil and Sand

Soil and sand samples are easily scanned. Light-colored samples require a black background. Scans like this are important for soil science, since they allow different specimens to be compared under identical lighting conditions.

As with all scans, the colors of scanned soil and sand samples might need to be adjusted. For example, when I scanned samples of light-colored sand from three locations (Figure G), the sand that looked whitest to the unaided eye was not as white when scanned.

Water can cause the color of soil and sand to change appreciably, and a scanner allows both wet and dry specimens to be scanned simultaneously.

Tree Rings

In MAKE, Volume 19, I described how to scan the annual growth rings in tree trunks and branches so they can be analyzed with ImageJ photo analysis software. Briefly, use a sharp, fine-toothed wood saw to cut sections from branches and trunks. Sand the exposed face of a section with 100-grit paper followed by 220-grit. The final polish is made with 400- or 600-grit paper.

Wood that was cut green should be allowed to dry for at least a day before sanding. You can enhance the appearance of the rings by moistening the face of the sample to be scanned.

Microbe Cultures

Bacteria and mold cultures are easily saved by digital scanning. My daughter Sarah’s discovery of living microbes in biomass smoke arriving in Texas from the Yucatan Peninsula was made possible by exposing Petrifilms (made by 3M) to ambient air on days with and without smoke.

(See the article: Sarah A. Mims and Forrest M. Mims III, Fungal spores are transported long distances in smoke from biomass fires, Atmospheric Environment 38, 651–655, 2004,

To confirm her discovery, Sarah exposed Petrifilms to smoke from burning grass and to nearby clean air. The films exposed to clean air had only a few bacteria and mold colonies. Those exposed to smoke had dozens of colonies — plus black ash from the burnt grass. Scans of these films provided persuasive evidence of the presence of microbes in biomass smoke.

Notes, Sketches, and Drawings

Field notes and sketches can be easily scanned for posting on the web or sending to friends, or to simply provide backup.

My ambition is to scan all of my field trip notebooks and photographic slides and prints and the thousands of log sheets on which I’ve recorded sun and sky data since May 1988. This will be a major chore that will require at least 10GB of storage. But the entire collection will fit on a tiny flash drive instead of a couple of heavy file cabinet drawers.

Going Further

Some specimens benefit from the inclusion of a scale in the scanned image. If the scale isn’t perfectly straight, you can straighten the image in a photo processing program.

You can use free, powerful ImageJ software (download it at to analyze your scanned images. (See my column in MAKE, Volume 18, for details about using ImageJ.)

Finally, there are many non-science applications for digital scanners that go well beyond making copies of documents and photos. For example, collectors of stamps and coins can easily digitize their collections.

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Forrest M. Mims III

Forrest M. Mims III (, an amateur scientist and Rolex Award winner, was named by Discover magazine as one of the “50 Best Brains in Science.” His books have sold more than 7 million copies.

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