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High Throughput Plant Phenotyping

The term “high throughput plant phenotyping” describes a rapidly developing branch in plant phenomics. It relies on technology for automated trait analysis as key feature for the generation of phenotypic data. May it be for for classical breeding, gene mapping or phene to gene approaches.

High throughput phenotyping affords methods and technical gear for automated sensing, data acquisition, data analysis,as well as plant transportation. In brief, for plant phenotyping “high throughput” denotes all technological means that achieve measuring more samples and / or more data points compared to the capabilities of manual measurements.

What is gained by the automation of phenotyping, besiedes saving human labour?

Automated measurements replace human labour (manual assessment of plant traits) for good reasons. The most prominent reason is to generate more data in less time. This is either achieved by investigating more plants, or by the application of more sensors that deliver data for more phenotypic result parameters. But automation yields more than throughput. Fixed automation routines and analysis protocols lead to better result reproducibility. Even simple traits that might be faster assessed by human observers, like shoot length, are measured more objectively and reliable.

A high number of individual samples

A high number of individual samples to analyse. A single run of a LemnaTec Lab Scanalyzer HTS or Phenocenter can screen more than hundreds or even thousands of samples in trays or multi-well plates. A fully automated Greenhouse Scanalyzer can capture multiple phenotypic data of hundreds of plants day by day. Germination Scanalyzers can measure germination rates in hundreds of seed germination trays in contineous operation.

Comprehensive phenotypic fingerprints

Regardless the sample size a combination of imaging sensors can facilitate comprehensive phenotypic fingerprints. Digital images allow to examine traits that signal in visible light, infrared, near infrared, fluorescence, or hyperspectral ranges. Thousands of datasets per day are generated quickly and need to be handled appropriately in databases. The extent of data may also rise dramatically when raw data is processed. Thus a wide range of sensors and acquisition modes promote high data throughput at high temporal and spatial resolution.

High temporal resolution

Automated phenotyping is perfect for the observation of dynamic traits that are expressed in the course of plant growth and development. Measurement series with high temporal resolution can be acquired without demand for human operation. Many plant related phenotype parameters show a significant diurnal amplitude that can be addressed when measuring multiple times per day. Even a comparatively low number of plants can lead to vast datasets per day, when measured e.g. each hour or every second hour. Temporal resolution becomes especially important if environmental conditions change often and unpredictable, as it happens in when phenotyping under field conditions with a Field Scanalyzer system.


Already a hand-loaded Lab Scanalyzer can be used for phenotyping at increased throughput, depending on the combination of sample size, measurement frequency and analysed parameters. For instance, sets of seedlings, leaves, or fruit can be imaged rapidly and data are delivered for further analysis.

You need further information?

LemnaTec GmbH

Tel. +49 2408 93 83 000
Fax. +49 2408 93 83 300

LemnaTec Corporation

Tel. +1 919 7934372

High throughput plant phenotyping is applicable at any size scale and in all cases where comprehensive datasets are required to describe plants.

Kevin Nagel, PhD

Application Scientist

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Dr. Marcus Jansen

Chief Scientist - Biologist

+49 160 937 26564
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