Plant Image Analysis Plant Image Analysis


Busch lab @ Gregor Mendel Institute
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Scientific article
A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis.
R. Slovak, C. Göschl, X. Su, K. Shimotani, T. Shiina, W. Busch,
2014 , Plant Cell , 0(0), 0
View at publisher | Download PDF


The BRAT pipeline is streamlined towards high-throughput quantification of primary root traits in early root growth. The segmentation plugin of the BRAT pipeline reads a set of input images containing multiple plants and tries to detect the objects of interest (plants) in the image. It measures multiple basic traits of the primary root (e. g. root length, root width, root topology and growth direction) and writes the results into a file. Summary statistics for multiple individuals of one genotype are created too. The plugin is able to process both, independent images and time series images (in this case root growth rates are calculated automatically). The detection of roots is not dependent on their growth direction (i.e. it works for a gravitropic roots as well). There are only very few parameters, the user has to provide, before the plugin starts its work and the segmentation doesn’t require user interaction. Plug-ins for quality control of the results are included.

The plugins are developed for the platform independent and freely available Fiji image processing software that can be run on Windows, Linux and Mac OS. The image-processing can be alternatively performed on a compute cluster to decrease processing times and the authors can provide help installing the software on a cluster.

Source: BRAT Manual

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Operating system
windows, mac, linux,

open-source, freeware,

Measured variables
length, diameter, orientation,

Automation level

Plant requirements

Image requirements

Export formats

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