LemnaTec Software for Phenotyping and Seed Testing

Translating images into application-specific information

The core of all LemnaTec phenotyping and seed testing systems is a comprehensive software package that enables operating the sensing equipment, storing the data and metadata, access to all records, and analysis of data. Hardware- and sensor- controls depend on the system and are specifically adapted for each product and also for customized solutions.

For all camera recordings, dedicated data processing is available. This ranges from systematic file administration over image processing to advanced machine learning algorithms. The image data processing and analysis is the key component of the phenotyping and seed testing procedures. Advanced image processing algorithms combined with machine learning tools ensure target-oriented analysis of the recorded image data. The analytical software translates digital image data into biologically relevant information.

Processing tools deliver sample-related data (examples):

SensorRecorded parametersInformation to derive from parameters
Visible light cameraReflectance in visible light spectrum
(colour image)
Counts, dimensions, texture, colour; growth and developmental features, stress responses
Fluorescence camera
(with corresponding excitation light and filter)
Intensity and distribution of fluorescence lightPresence and distributions of fluorescencent pigments; stress and senescence
Camera for chlorophyll fluorescence dynamics (Kautsky/PAM)Photosystem II-related parametersPhotosynthetic capacity and activity; stress, pathogen responses
NIR camera with 1450 nm filterWater-content related NIR signalTissue moisture; water stress responses
IR cameraSurface heat emissionPlant temperatures, transpiration
Hyper-/multispectral cameraSpectrally resolved reflectancePhysiological parameters, vegetation indices
Laser scannerPoint clouds3D surface, height map, inclination map, convex hull; growth and developmental features

The parameters extracted from the camera recordings deliver phenotypic information. For this purpose, we deliver a toolbox phenotyping-related functions, e.g.:

  • Size, count, morphological parameters, and color of plants

  • Height and width

  • Plant organ specific parameters

  • Time course analyses, e.g. for growth rates

  • 3D data of plants

  • Stress and pathogen responses, e.g. color changes, fluorescence changes

  • Surface temperature

  • NIR reflectance as indicator for water content

  • Fluorescence intensity, e.g. biomarkers or chlorophyll

  • Chlorophyll fluorescence parameters as indicator of photosystem status and activity

  • Broad range of vegetation indices together with index calculator for customized indices – more than 60 pre-set vegetation indices available in the software package.

LemnaGrid offers access to LemnaTec customer specific machine learning based solutions.

Application Examples

LemnaTec software at work in plant- and seed- applications

Phenotyping of seedlings on petri dish

Assessing shoot and root traits of agar-grown seedlings with PhenoAIxpert: shoots and roots are recognized separately and measured for their individual size. In the current example, primary root length, secondary root length, and shoot area were measured for each seedling.

Artificial intelligence for seedling classification

Emerging seedlings consist of various parts, e.g. roots, shoots, or root hairs. With machine learning algorithms, SeedAIxpert can be trained to recognize each of these parts separately.

Seedlings on Agar Phenotyping

Arabidopsis growth assay

Trays with growing Arabidopsis plants were imaged with PhenoAIxpert and images were processed for plant growth, morphology and color. Individual plants were identified and phenotypic properties of their visible plant area were assessed. Such tests serve for e.g. candidate screening, genetic studies, treatment effects, environmental responses

Phenotyping Arabidopsis

Seed classification

Embryo and Endosperm are visible on the surface of maize seeds. Imaged and classified by SeedAIxpert, fractions of embryo and endosperm are measured for each seed.

Seedling emergence test

Oilseed rape germination was assessed in a seedling emergence test with seeds placed in substrate. Emerging cotyledons were recognized and measured for germination frequency and seedling quality.

Seedling emergence classified