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Urs Fischer Photo by Anna StromUrs Fischer talks up some hybrid aspen plants in a greenhouse at the Umeå Plant Science Centre at Umeå University in Sweden. Photo by Anna Strom©.

A study by Bio4Energy researchers and partners was recommended by F1000 faculty as an important article in biology. The Faculty of 1000, or F1000, is an international group of academics—faculty members—who have tasked themselves with identifying and recommending the best research output in biology and medicine when it comes to peer-reviewed scientific articles.

The study by This email address is being protected from spambots. You need JavaScript enabled to view it.and This email address is being protected from spambots. You need JavaScript enabled to view it. and others gives an overview of a new package of analytical tools for quantifying large amounts of cellular traits, called phenotypes, in plants such as trees. Using the tools, researchers will be able to extract quantitative data from raw images obtained using state-of-the-art fluorescent microscopy. This has not previously been possible and the researchers expect this feature to speed up the process where large amounts of quantitative information need to be assessed. Hall and Fischer are part of the research platform Bio4Energy Feedstock and affiliated with Umeå University and the Swedish University of Agricultural Sciences, respectively.

The F1000 faculty member making the recommendation, David G. Oppenheimer of the University of Florida at Gainsville, U.S.A. stated in his motivation:

"The authors' method allows segmentation of images obtained by laser scanning confocal microscopy (or other optical sectioning methods of fluorescently labelled material) followed by assignment of cell types using the Random Forest machine learning algorithm.... I expect that this package will be useful for large-scale quantitative trait loci mapping projects or any projects that require quantification of cellular phenotypes for thousands of individuals."

For his part Hall said the process of putting the analytical package together had been exciting and challenging both, as it had seen plant biologists concerned with fundamental science working together with engineers on the applied side of things. 

"Interdisciplinary studies create a challenge to bring researchers together to find a common language to speak", Hall said.

Both he and Fischer said that they and the other article authors were greatly pleased to be acknowledged by high-ranking academic body outside of their own networks.

"It's an honour to be recognised by an established peer-review website", such as the F1000 Prime, Hall said.


The article Precision Automation of Cell Type Classification and Sub-cellar Fluorescence Quantification from Laser Scanning Confocal Images was published with open access in Frontiers in Plant Science, 9 February 2016.

The following authors are acknowledged:

Hardy C. Hall, Umeå University, Sweden - Bio4Energy

Azadeh Fakhrzadeh, Centre for Image Analysis, Uppsala University, Sweden

Cris L. Luengo Hendriks, Centre for Image Analysis, Uppsala University, Sweden

Urs Fischer, Swedish University of Agricultural Sciences - Bio4Energy

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