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There’s an App for That! Digital Image Analysis Counts Flies

tray with black flies

Researchers at the University of Illinois at Urbana-Champaign studying black flies (family Simuliidae) and their effect on avian wildlife quickly discovered the need for an efficient method for quantifying their fly captures. As a solution, they turned to digital image analysis software ImageJ. They placed captured flies in trays in a single layer and photographed the trays, which they then fed into ImageJ for counting. Their methods are described in a new report published this week in the Journal of Medical Entomology. (Photo by Morgan Meador)

By Melissa Mayer

Melissa Mayer

Melissa Mayer

If you’ve ever found yourself staring at a ginormous pile of insects that need counting, good news: There’s an app for that.

It was precisely that sort of situation that inspired Christine Parker, doctoral candidate at the University of Illinois at Urbana-Champaign and graduate research assistant with the Illinois Natural History Survey, to try something new.

“After the first season of black fly sampling, we started working through the samples and opened up this one sample that was massive—like several thousand flies,” she says. “Between myself and a volunteer, we spent several hours counting flies in that single sample. It was that sample that prompted me to find a better way to count the flies.”

Morgan Meador

Morgan Meador

Christine Parker

Christine Parker

Parker and colleagues Morgan Meador and Jeffrey Hoover, Ph.D., presented the results of their foray into using digital image analysis for counting small arthropods in a study published Monday in the Journal of Medical Entomology. They found ImageJ—open source image processing software from the National Institutes of Health—reduced processing time and was nearly error-free. ImageJ has been used previously to count cells and biological particles as well as ecological samples like pollen grains and fish or mosquito eggs.

“I think the flexibility as a research tool is probably the most exciting aspect of digital image analysis,” says Parker. “We used digital image analysis for counting small insects, but this type of analysis can be adjusted in many ways to count or detect other objects of interest.”

Counting Crows Flies

To catch black flies (family Simuliidae) for counting, the research team baited CDC light traps with carbon dioxide from dry ice. The idea is to mimic the exhaled gases that let female black flies know they’ve come upon an animal that might be a good source for a bloodmeal, which she needs for her developing eggs.

The team euthanized the captured flies, removed any insects that did not appear to be black flies, and poured them into petri dishes, being careful to avoid overlap or clumping. Then, they took photos of the petri dishes with a digital camera mounted on a chemistry stand and fed those images into ImageJ.

Parker found the process unexpectedly smooth—which is a good thing since the team did this for 68 total samples. “I was first surprised at how simple the software was to use and then surprised that no one had used it for counting small insects,” she says.

The team found that the automated counts using ImageJ were nearly always identical to their manual counts—and when the counts differed, the automated counts skewed slightly more conservative. Larger samples with more than 100 flies were prone to a bit more error—but never more than 5 percent. The authors think this undercounting was likely caused by clumping or overlapping or perhaps debris in the viewing field. They recommend using several gridded petri dishes, spreading the samples out carefully, and fine-tuning the settings to optimize for the sample.

The research team didn’t record the time spent manually or automatically counting black flies, but they agree with other reports that ImageJ substantially cut down the time spent counting specimens. “In hindsight, I wish we had recorded the time we spent using each method because the manual counts took so much time,” says Parker. “Using our automated method, that sample might take half an hour to divide up flies, photograph, and run the software.”

Tech Supports Valuable Research

That saved time is a boon for researchers operating on small budgets—especially because ImageJ is free for scientists to use and doesn’t require specialized equipment. And, because the software is user-friendly and simple to operate, research teams may have more freedom to parcel those tasks out to less experienced members.

Ultimately, quicker counts could help researchers perform critical work like surveilling for insects that cause vector-borne diseases. Since arthropod vectors cause issues that range from nuisance problems to serious health risks for the livestock, wild animals, and humans they affect, that’s a big deal.

“Providing the relevant agencies—like health departments and the CDC—with up-to-date detection information about where and when vectors and associated pathogens are occurring can help prevent disease transmission and potentially improve diagnoses of vector-borne diseases,” says Parker.

Check out Parker’s black fly workshop to learn more about how the team used ImageJ and to get quick tips for preparing samples.

Journal of Medical EntomologyRead More

Using Digital Image Analysis to Quantify Small Arthropod Vectors

Journal of Medical Entomology


Melissa Mayer is a freelance science writer based in Portland, Oregon. Email:


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