Plant Image Analysis Plant Image Analysis


Leibniz Institute of Plant Genetics and Crop Plant Research

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Scientific article
HTPheno: an image analysis pipeline for high-throughput plant phenotyping.
A. Hartmann, T. Czauderna, R. Hoffmann, N. Stein, F. Schreiber,
2011 , BMC Bioinformatics , 12(0), 148
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HTPheno is an open source image analysis pipeline that supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.

It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening.

Source: HTPheno website

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Operating system
windows, mac, linux,


Measured variables
height, width, diameter, surface,

Automation level

Plant requirements

Image requirements
any, top-view, side-view,

Export formats
txt, csv, excell,

Other information