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New lab could speed up plant discoveries

PhenoSight uses advanced imaging technology to automate plant phenotyping.

Chris Torres, Editor, American Agriculturist

June 20, 2024

4 Min Read
 Plants on a conveyor belt at a phenotype facility
INSIDE PHENOSIGHT: Plants grow on a conveyor belt that moves them, on regular intervals, to two imaging stations, scales, and an automated watering and fertilizing station. Boyce Thompson Institute

Bringing a new generation of stress-tolerant plants to market is time-consuming and not for the faint of heart. A new lab recently opened at the Boyce Thompson Institute in Ithaca, N.Y., may help supercharge some of that process.

The BTI Plant Phenotyping Facility, also known as PhenoSight, uses advanced technology to analyze up to 64 large plants — up to 3 feet tall — or 1,280 smaller plants simultaneously, generating real-time data on plant health, vigor and other characteristics, a key step in the process of developing plants that are better able to handle drought and other stressors.

Magdalena Julkowska, assistant professor and lead researcher at the facility, says the goal is to speed up plant phenotyping to enable researchers to make new plant discoveries quicker.

What is phenotyping?

Simply put, phenotyping is the process of measuring and analyzing observable plant characteristics.

Much of this work is done taking photographs of plants in various growth stages, or going out and physically handling plants to get specific growth measurements.

With photosynthesis, for example, researchers use portable machines to go out and measure chlorophyll, which absorbs light in the photosynthetic process. But this can be time-consuming, taking up to 30 minutes to measure a single plant.

Using PhenoSight, all this is done using imaging technology.

“We don’t need to physically take any leaves from the plant, so it takes us much less time to get your data,” Julkowska says. “And also, because we are doing it nondestructively, we can measure a much higher number of replications and genotypes."

“Using imaging technology like this, you can measure photosynthesis, chlorophyll content, photosynthetic activity and more across the entire plant without the clippings, and you can see if younger leaves are reacting to a certain stressor differently than an old leaf, or vice versa,” she adds. “You can gain much more insights with those kinds of technologies than you would do using more traditional approaches by integrating advanced chlorophyll fluorescence and RGB imaging to get real-time data on plant health and vigor.”

How it works

Plants grow on a conveyor belt that moves them, on regular intervals, to two imaging stations, scales, and an automated watering and fertilizing station.

PhenoSight has multiple systems. Its high-throughput imaging system allows the plants to move through a dark-light adaptation tunnel, which is useful to measure maximum level of photosynthesis, as the plants must be adapted to darkness. The tunnel allows researchers to adapt multiple plants to darkness at one time.

The plants then move to a 440-pound multispectral camera that moves up and down, flashing the plants with a variety of light types, wavelengths and intensity to measure chlorophyll fluorescence at various light intensities.

Finally, the plants move to an RGB and chlorophyll fluorescence station where they are imaged from top and side view using both cameras, allowing researchers to extract traits like digital plant biomass — an approximation of how big the plant is — without cutting it down. The chlorophyll fluorescence camera serves the purpose of masking, which essentially extracts the pixels belonging to the plant from the pixels in the background.

“This station provides us an automatic calculation for simple plant traits, such as plant height, width, area and so on. The plant height is used in the next round by multispectral camera to adjust its vertical position, so we measure the photosynthetic efficiency with highest possible accuracy,” Julkowska says.

The plants can also be weighed, watered or fertilized using an automated watering and weighing unit.

“This allows us to apply stresses in a very consistent manner, and also measure how much water the plants lose between the watering rounds, allowing us to see how they react to drought and wet conditions,” Julkowska says.

The system can capture plant responses every two hours, which she says allows researchers to capture images of plants over time to study plant growth and development, as well as plant responses to environmental stresses.

Why it matters

Most of the research done at BTI is at the discovery stage. For example, Julkowska’s work focuses on salt and drought stress to try and understand genes that contribute to this tolerance in order to future-proof plants for climate change.

Her goal is to find a wild or indigenous plant species that is tolerant and either adapt it to ag production or translate its mechanisms into existing plants.

Using advanced phenotyping, she says, speeds up this process.

“The machine is saving us tremendous amount of time and effort with that,” Julkowska says. “In order to phenotype every day, it would take at least four hours to do what the machine does in less than two hours, and we would be studying a tiny portion of one leaf rather than responses at the whole canopy level.”

About the Author(s)

Chris Torres

Editor, American Agriculturist

Chris Torres, editor of American Agriculturist, previously worked at Lancaster Farming, where he started in 2006 as a staff writer and later became regional editor. Torres is a seven-time winner of the Keystone Press Awards, handed out by the Pennsylvania Press Association, and he is a Pennsylvania State University graduate.

Torres says he wants American Agriculturist to be farmers' "go-to product, continuing the legacy and high standard (former American Agriculturist editor) John Vogel has set." Torres succeeds Vogel, who retired after 47 years with Farm Progress and its related publications.

"The news business is a challenging job," Torres says. "It makes you think outside your small box, and you have to formulate what the reader wants to see from the overall product. It's rewarding to see a nice product in the end."

Torres' family is based in Lebanon County, Pa. His wife grew up on a small farm in Berks County, Pa., where they raised corn, soybeans, feeder cattle and more. Torres and his wife are parents to three young boys.

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