Portable PathoScan device diagnoses crop diseases in the field

Say you suspect a serious crop disease in your field. The usual process is to send plant samples to a diagnostics laboratory – usually in a city — to verify or rule out the disease.

However, due to logistics, it can take a lab anywhere from days to weeks to get back with a diagnosis. So what happens if you need it sooner so you can make crucial management decisions?

Ethan Done wants to help farmers in those scenarios by bringing the same technology employed by urban labs to the farm field.

Why it Matters: Most crop disease diagnostic tests take place in government-approved laboratories. However, the time taken for a lab to identify a pathogen from a sample may compromise a grower’s ability to take action on a fast-spreading crop disease.

Done is the chief operating officer and co-founder of Saskatoon-based startup PathoScan Technologies. Along with co-founder Tayab Soonro, Done invented a portable, lunchbox-size device called the PathoBox, which is intended to allow farmers to test and identify crop disease in less than two hours. Together with the PathoKit, it comprises the PathoScan system.

The findings also help farmers use chemical controls only where they’re needed.

“I saw that there was a problem and I wanted to help, which is what sparked the idea for a solution that’s smaller, mobile, lightweight and more affordable for the average producer,” wrote Done in a news release.

The development funding for the PathoScan is being provided by Mitacs, a “national innovation connector” funded by federal, provincial and territorial governments.

“Mitacs is proud to be part of the PathoScan story. It’s a great example of innovation and Saskatchewan’s Growth Plan at work,” Mitacs chief executive officer Stephen Lucas wrote.

Guided by farmer input

A lifelong resident of Saskatoon, Done has been around the ag world his whole life, thanks to family working in agriculture and related fields.

His path to the PathoScan started in 2022 in his first year at the University of Saskatchewan (from which he graduated with a B.Sc. in biochemistry, microbiology and immunology) when Agriculture Canada’s research centre in Saskatoon offered him an internship diagnosing plant diseases.

One of his duties was demonstrating the government’s pathogen testing service — a polymerase chain reaction (PCR) test called loop-mediated isothermal amplification (LAMP) — at agricultural events. The interest from producers came fast, but he had to tell them the devices on display were for lab use only.

“We went out to Ag in Motion and there was a lot of producers that wanted to buy what we were doing,” he said.

Seeing the demand, Done and Soonro developed the idea for the PathoScan and won a funding competition held by the U of S. They used the proceeds to develop a prototype, a process that depended on producer feedback.

“We didn’t change any of the underlying biology.… We just found every point where something could go wrong or something was made hard or something was not optimized to be used in the field and tried to work with producers to figure it out.”

One issue they had to tackle was ice. For hydration reasons, the parts of the LAMP PCR test are sent to labs frozen, which is a no-go for farmers and agronomists using it in the field.

“If you’re driving around the field for four hours or whatever, you have to have it kept in ice, and that’s obviously a problem.

“So the first thing we did is we actually figured out a way to dry out that reaction, and so basically you get to the field and before you start using it, you just rehydrate it. We have a little dropper and you just add a drop of water and, it rehydrates it so you don’t have to worry about ice.”

In addition to making the unit more compact than its lab-stationed counterparts, Done and Soonro also simplified instructions and modified some of the parts, such as increasing the size of the testing tubes to make them harder to lose.

How it works

Using the PathoBox is fundamentally simple. The user fills a reaction tube with a chemical powder-water mixture comprised of synthetic crop disease DNA and crushed plant pieces. The tube is placed into the device, heating the contents and using a molecular technique to make millions of copies of any pathogen DNA on the plant.

The process takes less than an hour. If the pathogen levels are high, the liquid in the tube changes colour, signaling disease presence.

“We can create whatever synthetic DNA we want so we can — in theory — do any pathogen, whether it’s a virus, whether it’s sclerotinia, aphanomyces. We can even do things like detecting GMO crops.”

The PathoScan can also test for other Prairie heavy hitters such as fusarium graminearum, fusarium wilt and grey mould.

AI to expand capacity

Next up for Done is the development of an accompanying AI-driven vision system that not only offers the ability to watch the process but also strengthens PathoScan’s capacity as an agronomic insight tool.

“Right now, it’s a positive or negative: does it have the pathogen or does it not?” he said.

“What the AI system would actually allow us to do is watch the reaction as it happens, and so I would be able to say in each plant how much pathogen there was. And that would be able to help us refine our, ‘should you spray or should you not spray?’ sort of dichotomy.”

To enable field testing far away from wi-fFi sources, the AI component will run on a chip in the machine.

“We’re trying to build something into the hardware that doesn’t need wi-fi because we want it to work in the field.”

Weston Bohachewski, an agronomist with Shark Ag Consulting in Melfort, Sask., has used a prototype of the PathoScan for the past couple of fungicide seasons and enjoys the freedom it gives him to quickly make suggestions to clients.

“We’ve run into issues before where, maybe on a Friday afternoon, the farmer wants to get field tested. Well, we’re not getting results back for three or four business days; we won’t have it back (until) maybe Thursday of the next week, and then sometimes … it’s past the idea of spray time, so that’s where the machine is fitting in.”

If he has a complaint about the unit, it’s its inability to measure disease intensity, a weakness Done hopes to correct with his AI system. Otherwise, he likes how it takes the guesswork out of pathogen identification.

Mitacs is funded by the governments of Canada, Alberta, British Columbia, New Brunswick, Newfoundland and Labrador, Nova Scotia, Ontario, Quebec, Saskatchewan and Yukon as well as Innovation PEI and Research Manitoba.