Phenotyping Software Comes to Vienna Biocenter

Published online: Oct 13, 2015
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LemnaTec OS, the phenotyping software system from biotech company LemnaTec GmbH, has been deployed at the Vienna Biocenter with a growth chamber designed to simulate different climates and stress conditions.

The Vienna Biocenter (VBC) in Austria, is a leading international biomedical research centers and employs around 1,400 scientists and 700 students. Specializing in life sciences, VBC hosts a broad spectrum of research institutions including the Gregor Mendel Institute, Max F. Perutz Laboratories, Institute of Molecular Biotechnology, Institute of Molecular Pathology and a University of Applied Sciences.

Scientists from more than 40 nations help to create a research environment that is constantly changing and expanding. To date, members of the VBC community have received 31 European Research Council grants and 11 Wittgenstein awards.

Crucial to its success is the VBC’s excellent research infrastructure, which is provided by Campus Science Support Facilities GmbH (CSF), a publicly funded, non-profit organization operating within the VBC campus. CSF comprises 10 facilities including Protein Technologies, Next Generation Sequencing and Bioinformatics & Scientific Computing.

Jakub Jez is head of the Plant Science Facility, which provides professional support to research groups at the VBC as well as external customers. This facility operates 22 plant growth chambers capable of simulating many different environmental conditions, such as low and high temperatures, specific light spectra and different gas conditions. One of the growth chambers is equipped with an automated plant phenotyping system.

“The phenotyping chamber was designed and built by the Gregor Mendel Institute,” says Jez. “To complete the picture, we needed robust software to accurately process the high volumes of data we were generating. Although there are lots of freeware packages now available, we found that these usually require a lot of manual intervention to produce meaningful results and functionality is often limited.

“We met LemnaTec at the PhenoDays conference, and we were very impressed with the LemnaTec OS software system,” Jez continues. “Although what it does is extremely complex, basic image analysis can be performed very easily. When we deployed the software, it was a success from the start. After a couple of days, we were able to get our first set of data; after two weeks we had perfect image analysis results.”

The chamber accommodates 1,260 Arabidopsis plants, and image acquisition is conducted several times per day. Very large numbers of images are then exported to LemnaTec OS for detailed analysis. Projected leaf area, plotted over time, provides information about individual plant growth behavior. Plants can then be grouped accordingly by various morphological features. The LemnaTec software then accesses morphometric and color parameters complementing the leaf area information.