Limits...
HTPheno: an image analysis pipeline for high-throughput plant phenotyping.

Hartmann A, Czauderna T, Hoffmann R, Stein N, Schreiber F - BMC Bioinformatics (2011)

Bottom Line: 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.HTPheno is applied to analyse two barley cultivars.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany.

ABSTRACT

Background: In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms.

Results: This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. 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. HTPheno is applied to analyse two barley cultivars.

Conclusions: HTPheno, an open source image analysis pipeline, 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.

Show MeSH
Comparison of different barley (Hordeum vulgare) cultivars. Habitus of cultivar Barke and of cultivar Morex in side view (A, B). Plot of the average projected shoot area in side view of 312 barley plants composed of the two cultivars with 78 Barke plants and 78 Morex plants under well watered conditions (solid line) and 78 Barke plants and 78 Morex plants under drought stressed conditions (dashed line). Both cultivars have lesser average projected shoot area under drought stress conditions but approximate to plants under well watered conditions in the last days of the experiment (C). The average projected shoot area of cultivar Morex is under both conditions larger. Vertical bars show ± S.E. of 78 replicates. Analysis was carried out with HTPheno.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3113939&req=5

Figure 5: Comparison of different barley (Hordeum vulgare) cultivars. Habitus of cultivar Barke and of cultivar Morex in side view (A, B). Plot of the average projected shoot area in side view of 312 barley plants composed of the two cultivars with 78 Barke plants and 78 Morex plants under well watered conditions (solid line) and 78 Barke plants and 78 Morex plants under drought stressed conditions (dashed line). Both cultivars have lesser average projected shoot area under drought stress conditions but approximate to plants under well watered conditions in the last days of the experiment (C). The average projected shoot area of cultivar Morex is under both conditions larger. Vertical bars show ± S.E. of 78 replicates. Analysis was carried out with HTPheno.

Mentions: The application example shown in Figure 5 represents the comparison of different barley (Hordeum vulgare) cultivars. Both cultivars Barke and Morex are precisely defined homozygous genotypes. Barke plants are identical among each other and Morex plants are identical among each other, but Barke and Morex do not correspond. They are 99.9 percent genetically identical, but vary widely in morphological characteristics. The habitus of cultivar Barke has semi-dwarfed growth and develops thin leaves. To compensate the semi-dwarfed growth Barke plants tiller (see Figure 5A). Morex plants by contrast grow higher and develop leaves with larger area (see Figure 5B).


HTPheno: an image analysis pipeline for high-throughput plant phenotyping.

Hartmann A, Czauderna T, Hoffmann R, Stein N, Schreiber F - BMC Bioinformatics (2011)

Comparison of different barley (Hordeum vulgare) cultivars. Habitus of cultivar Barke and of cultivar Morex in side view (A, B). Plot of the average projected shoot area in side view of 312 barley plants composed of the two cultivars with 78 Barke plants and 78 Morex plants under well watered conditions (solid line) and 78 Barke plants and 78 Morex plants under drought stressed conditions (dashed line). Both cultivars have lesser average projected shoot area under drought stress conditions but approximate to plants under well watered conditions in the last days of the experiment (C). The average projected shoot area of cultivar Morex is under both conditions larger. Vertical bars show ± S.E. of 78 replicates. Analysis was carried out with HTPheno.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113939&req=5

Figure 5: Comparison of different barley (Hordeum vulgare) cultivars. Habitus of cultivar Barke and of cultivar Morex in side view (A, B). Plot of the average projected shoot area in side view of 312 barley plants composed of the two cultivars with 78 Barke plants and 78 Morex plants under well watered conditions (solid line) and 78 Barke plants and 78 Morex plants under drought stressed conditions (dashed line). Both cultivars have lesser average projected shoot area under drought stress conditions but approximate to plants under well watered conditions in the last days of the experiment (C). The average projected shoot area of cultivar Morex is under both conditions larger. Vertical bars show ± S.E. of 78 replicates. Analysis was carried out with HTPheno.
Mentions: The application example shown in Figure 5 represents the comparison of different barley (Hordeum vulgare) cultivars. Both cultivars Barke and Morex are precisely defined homozygous genotypes. Barke plants are identical among each other and Morex plants are identical among each other, but Barke and Morex do not correspond. They are 99.9 percent genetically identical, but vary widely in morphological characteristics. The habitus of cultivar Barke has semi-dwarfed growth and develops thin leaves. To compensate the semi-dwarfed growth Barke plants tiller (see Figure 5A). Morex plants by contrast grow higher and develop leaves with larger area (see Figure 5B).

Bottom Line: 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.HTPheno is applied to analyse two barley cultivars.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany.

ABSTRACT

Background: In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms.

Results: This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. 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. HTPheno is applied to analyse two barley cultivars.

Conclusions: HTPheno, an open source image analysis pipeline, 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.

Show MeSH