plant imaging consortium

Plant biologists welcome their robot overlords

Thursday, February 16, 2017

Old-school areas of plant biology are getting tech upgrades that herald more detailed, faster data collection.

by Heidi Ledford

25 January 2017
 
A robot measures the crops in an agricultural field near Columbia, Missouri (credit: DeSouza/Fritschi/Shafiekhani/Suhas/University of Missouri)
 
As a postdoc, plant biologist Christopher Topp was not satisfied with the usual way of studying root development: growing plants on agar dishes and placing them on flatbed scanners to measure root lengths and angles. Instead, he would periodically stuff his car with plants in pots dripping with water and drive more than 600 kilometres from North Carolina to Georgia to image his specimens in 3D, using an X-ray machine in a physics lab.
 

Five years later, the idea of using detailed imaging to study plant form and function has caught on. The use of drones and robots is also on the rise as researchers pursue the ‘quantified plant’ — one in which each trait has been carefully and precisely measured from nearly every angle, from the length of its root hairs to the volatile chemicals it emits under duress. Such traits are known as an organism’s phenotype, and researchers are looking for faster and more comprehensive ways of characterizing it.

From 10 to 14 February, scientists will gather in Tucson, Arizona, to compare their methods. Some will describe drones that buzz over research plots armed with hi-tech cameras; others will discuss robots that lumber through fields bearing equipment to log each plant’s growth.

The hope is that such efforts will speed up plant breeding and basic research, uncovering new aspects of plant physiology that can determine whether a plant will thrive in the field. “Phenotype is infinite,” says Topp, who now works at the Donald Danforth Plant Science Center in St Louis, Missouri. “The best we can do is capture an aspect of it — and we want to capture the most comprehensive aspect we can.”

The plummeting cost of DNA sequencing has made it much easier to find genes, but working out what they do remains a challenge, says plant biologist Ulrich Schurr of the Jülich Research Centre in Germany. “It is very easy now to sequence a lot of stuff,” he says. “But what was not developed with the same kind of speed was the analysis of the structure and function of plants.”

Plant breeders are also looking beyond the traits they used to focus on — such as yield and plant height — for faster ways to improve crops. “Those traits are useful but not enough,” says Gustavo Lobos, an ecophysiologist at the University of Talca in Chile. “To cope with what is happening with climate change and food security, some breeders want to be more efficient.” Researchers aiming to boost drought tolerance, for example, might look at detailed features of a plant’s root system, or at the arrangement of its leaves.

False-colour images of a bean-breeding trial captured by a camera mounted on a drone (credit: Lav R. Khot/Washington State University & Phillip N Miklas/USDA-ARS)

A need for speed

The needs of these researchers have bred an expanding crop of phenotyping facilities and projects. In 2015, the US Department of Energy announced a US$34-million project to generate the robotics, sensors and methods needed to characterize sorghum, a biofuel crop. Last year, the European Union launched a project to create a pan-European network of phenotyping facilities. And academic networks have sprung up around the globe as plant researchers attempt to standardize approaches and data analyses.

Large-scale phenotyping has long been used in industry, but was too expensive for academic researchers, says Fiona Goggin, who studies plant–insect interactions at the University of Arkansas in Fayetteville. Now, the falling prices of cameras and drones, as well as the rise of the ‘maker’ movement that focuses on homemade apparatus, are enticing more academics to enter the field, she says.

At Washington State University in Pullman, biological engineer Sindhuja Sankaran’s lab is preparing to deploy drones carrying lidar, the laser equivalent of radar. The system will scan agricultural fields to gather data on plant height and the density of leaves and branches. Sankaran also uses sensors to measure the volatile chemicals that plants give off, particularly when they are under attack from insects or disease. She hopes eventually to mount the sensors on robots.

A drone loaded with thermal imaging equipment flies over grapevines (credit: Lav R. Khot/Washington State University)

Sankaran’s mechanical minions return from their field season with hundreds of gigabytes of raw data, and analysing the results keeps her team glued to computers for the better part of a year, she says. Many researchers do not realize the effort and computing savvy it takes to pick through piles of such data, says Edgar Spalding, a plant biologist at the University of Wisconsin–Madison. “The pheno­typing community has rushed off to collect data and the computing is an afterthought.”

Standardizing the technology is another barrier, says Nathan Springer, a geneticist at the University of Minnesota in St Paul. The lack of equipment everyone can use means that some researchers have to rely on slower data-collection methods. Springer has been working with 45 research groups to characterize 1,000 varieties of maize (corn) grown in 20 different environments across the United States and Canada. The project has relied heavily on hand measurements rather than on drones and robots, he says.

Topp now has his own machine to collect computed tomography (CT) images, but processing samples is still a little slow for his liking. He speaks with reverence of a facility at the University of Nottingham, UK, that speeds up its scans by using robots to feed the plants through the CT machine. But he’s pleased that he no longer has to haul his soggy cargo across three states to take measurements. “It’s just endless, the number of possibilities.”

Nature 541, 445–446 (26 January 2017) | doi:10.1038/541445a

Plant Imaging Consortium Seed Grants Announced

Thursday, December 17, 2015

The Plant Imaging Consortium, Missouri-Arkansas NSF EPSCoR Track-2 program, has selected five competitive seed grant proposals to fund in 2015-2017:

1) Stephen Grace – “Using Plant Phenotyping, RNA Sequencing, and Metabolomics to Identify Drought Tolerance Mechanisms in Tomato”

University of Arkansas at Little Rock, Little Rock, AR

Co-PIs (collaborators): Argelia Lorence, Arkansas State University, Jonesboro, AR

             Christopher Topp, Donald Danforth Plant Science Center, St. Louis, MO

2) Vibha Srivastava – “A Cre-ative approach of imaging stress responses at the molecular level: amplifying gene expression in response to stress”

University of Arkansas, Fayetteville, AR

Collaborators: Raman Sunkar, Oklahoma State University, Stillwater, OK

              Fiona Goggin, University of Arkansas, Fayetteville, AR

3) Benjamin Babst – “A Role for Transport in Nitrogen Stress Tolerance”

University of Arkansas at Monticello, Monticello, AR

Co-PI: Fei Gao, University of Arkansas at Monticello, Monticello, AR

4) Noah Fahlgren – “PlantCV Extension and Expansion for Plant Imaging Consortium Compatibility”

Donald Danforth Plant Science Center, St. Louis, MO

Co-PI: Malia Gehan, Donald Danforth Plant Science Center, St. Louis, MO

Collaborators: Jackson Cothren and Chris Angel , Center for Advanced Spatial Technologies, University of Arkansas

                          Argelia Lorence and Suxing Liu , Department of Chemistry and Physics, Arkansas State University

                          Yuan-Chuan Tai , Department of Radiology, Washington University in St. Louis

5) Margaret Frank – “Graft junction formation: a dynamic investigation using PET and confocal imaging”

Donald Danforth Plant Science Center, St. Louis, MO

Co-PIs: Christopher Topp, Donald Danforth Plant Science Center, St. Louis, MO

             Dan Chitwood, Donald Danforth Plant Science Center, St. Louis, MO

PIC received many competitive proposals from institutions across Missouri and Arkansas.  These proposals aimed to do collaborative reserach on bioimaging using PIC facilitites at various research institutions in Missouri and Arkansas.

What’s Happening in the Plant Phenotyping World

Tuesday, July 7, 2015

PhenoDays 2015 in Munich, Germany

PhenoDays 2015: October 28 – 30, 2015 at Marriott Hotel Freising, near Munich Airport, Germany

Registration is open now.  All speakers should submit an abstract by September 1, 2015.

In the era of Plant Genomics the amount of DNA information of crops has increased enormously. As a consequence, more effective and reliable phenotyping data has become the bottleneck for modern genetic crop improvement. Therefore Plant Phenotyping has become a major field of research in plant breeding.

In order to meet the challenges of this very new and promising field of research new technologies such as greenhouse automation and plant imaging systems in controlled environments and in the field are needed.

The PhenoDays International Symposium exactly addresses the Phenotyping bottleneck by providing stimulating talks from internationally renowned keynote speakers from the seed industry, breeding institutes and academic breeding groups working in the Plant Phenotyping research area.

This surely is a great opportunity for the researchers from all over the world to meet and exchange their ideas, approaches and results in Plant Phenotyping research.

Phenomics: How Next-Generation Phenotyping is Revolutionizing Plant Breeding

This book represents a pioneer initiative to describe the new technologies available for next-generation phenotyping and applied to plant breeding. Over the last several years plant breeding has experienced a true revolution. Phenomics, i.e., high-throughput phenotyping using automation, robotics and remote data collection, is changing the way cultivars are developed. Written in an easy to understand style, this book offers an indispensable reference work for all students, instructors and scientists who are interested in the latest innovative technologies applied to plant breeding.

Publisher: Springer; 2015 edition (January 13, 2015)
Language: English ASIN: B00S7L0DDI

Lemnatec Resources

News on Plant Phenotyping Image Processing Applications here

Application Note – Analysing Turfgrass Images
Application Note – Biocide screening
Application Note – Color Analysis using LemnaGrid

More LemnaTec News, including research, conferences, courses and workshops can be found here

Searching for a Job?

Field Phenotyping Image Analysis & Data Handler position at Rothamsted Research.  If interested, please visit http://www.rothamsted.ac.uk/jobs/1392

This post requires expertise in image processing and analysis, software and database development, preferably with a plant/agricultural science background, and will involve data extraction and large scale high throughput data handling. The appointee will liaise with other team members and facility users to ensure high throughput automated pipelines are in place to facilitate data flow from the experiments to the experimentalists.

Plant Imaging Consortium Annual Meeting

Event date(s): Monday, June 5, 2017 to Tuesday, June 6, 2017
Location: Hilton St. Louis at the Ballpark, St. Louis, MO


Plant Imaging Consortium/LemnaTec Internship - Summer 2017

Event date(s): Friday, May 5, 2017
Location: Research Triangle Park


Summary

The Plant Imaging Consortium (PIC), a program funded by the NSF EPSCoR RII Track 2 program, and LemnaTec have joined forces and are offering a unique summer internship opportunity for a graduate student affiliated with one of the PIC partner institutions in Arkansas or Missouri to gain experience in the exciting field of plant high throughput phenotyping. The selected candidate will work with LemnaTec Corporation in North America to produce high quality documents that facilitate external and internal customer product familiarity and ease of equipment use.

Functional Competencies

The selected candidate will:

  • Assist with the creation of user manuals, maintenance manuals, parts and schematics manuals, troubleshooting guides, installation guides and other information products as necessary. 
  • Interview and work closely with engineers and other technical personnel and use knowledge of plant phenotyping hardware and software systems to ensure accuracy and completeness of information. 
  • Research and draw relevant information from vendor documentation, engineering specifications, and existing product documentation, as appropriate. 
  • Effectively use appropriate authoring techniques, tools, standards, and processes to create documentation deliverables. 
  • Assist in creation of graphics in conjunction with design concepts and templates. 
  • Work independently as well as part of a technical communication team. 
  • Report the progress of assigned tasks against defined schedules.

Internship Start Date

Thursday, June 1, 2017

Duration of the internship

6 weeks

Location

LemnaTec North America (Research Triangle Park) and visit(s) to multiple locations across the US

This internship includes a competitive stipend ($4,000), housing allowance (~$3,000), and travel support ($6,000) provided by PIC and LemnaTec.

Interested candidates must submit a CV and a letter of recommendation to alorence [at] astate [dot] edu">alorence [at] astate [dot] edu and todd [dot] dezwaan [at] lemnatec [dot] com">todd [dot] dezwaan [at] lemnatec [dot] com by May 5, 2017.