LemnaTec Phenotyping Software

The core of all LemnaTec phenotyping systems is a comprehensive software packages that enable operating the sensing equipment, storing the data and metadata, access to all records, and analysis of data.
The software controls and monitors the mechanical hardware and the sensor packages. For each camera or scanner in all LemnaTec systems, a pre-set on-purpose protocol can be established for all measurements. This can include camera settings, such as shutter or iris control or triggering of the corresponding light sources.
For all camera recordings, dedicated data processing is available. The data processing and analysis is the key component of the phenotyping procedure. 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

In automatic phenotyping systems, users can schedule operation of the system and trigger measurements with the mounted sensors. Any automated hardware can operate in a time-scheduled mode for repeated programmed actions such as moving the sensing equipment to defined places and start camera recording. Thus, time- and space- resolved experiment planning is enabled.

All settings and recordings are stored in a central database. These data can be accessed via a dedicated interface that allows data retrieving. Retrieved data can be processed with the provided data analysis tools. The output of the analyses is corresponding to the capabilities of the cameras used for the recording. The analysis tools provide a large set of drag-and-drop functions for image processing that enable users to establish customized analysis procedures. In addition, case-specific analyses can be ordered from LemnaTec that allow one-click analyses of standard procedures, such as germination testing.

The analysis tools include machine learning and thereby give access to advanced classification even in complex cases. All processing results are stored in the database, together with the original data and metadata.

Illustration of software modules for data acquisition, processing, management and analysis operated on dedicated computer hardware

The LemnaTec software consists of the following modules
that serve for the tasks as described above:

Hardware Control and data acquisition:

The LemnaControl software module controls and monitors all required hardware components such as cameras, illumination, conveyor belts, pumps and scales. It enables trained operators to efficiently run the Germination Scanalyzer system with only few technical and IT background.

LemnaControl facilitates rapid and easy initiation of experiments with specific configurations on the LemnaTec systems. During an experiment, all data for an individual tray are stored in the central database.

LemnaControl facilitates flexible operating modes, as part of the overall experimental. Those can be scheduled for an entire experiment, with repeating tasks e.g. individual tasks such randomizing the tray position in the system.

LemnaControl can be supervised remotely by the operator. Visualization of all processes, error diagnostics, logging and alerting are standard features of the LemnaControl software.

Data storage and backup:

The core database structure is based on SQL Database technology (either Oracle or Postgres) and can handle very large datasets. The open interface allows direct integration into any customer IT infrastructure such as e.g. LIMS environments.

Image viewer and data management:

The LemnaBase software module facilitates rapid and easy visualization of images acquired during an experimental run. Flexible viewing schemes allow direct comparison of multiple plant simultaneously. LemnaBase further allows to import images into the database and likewise export them. New databases can be created, and data be transferred.

Image Analysis and feature extraction:

The LemnaGrid software module uses a graphical programming environment (similar to LabView or Microsoft Robotics Studio), which allows easy integration of different image analysis algorithms. The image processing pipeline extracts desired properties/features from the original image and stores results in the central database. LemnaGrid uses state-of the art machine and deep learning tools, besides classical image analysis to detect germination features.

Data Analysis and visualisation:

The R software allows easy integration of data analysis algorithms, which are available from the scientific community and well documented. Dedicated R packages allow combination, aggregation and visualization of large data sets.


Phenotyping Software

LEMNATEC-OS is a complete open software system for phenotyping plants, seeds and small organisms. A suite of integrated modules enables scientists to automate phenotyping processes and analyse the resulting images. Using drag-and-drop functionality, complex algorithms can be quickly constructed, modified and tested.

The APPLICATIONS section of this website shows some of the ways this powerful software suite can be used to measure specific characteristics and traits in plant phenotyping.

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Integrated Software Modules

  • Control movement of plant carriers and sensors
  • Plan and perform routines for watering, spraying and imaging
  • API for integration of a wide range of sensors
  • Programmable interface for non-LemnaTec equipment
  • Centralised data acquisition
  • Graphical process for detailed image analysis
  • Wide range of image formats
  • Library of image processing algorithms including hyperspectral data
  • API for integration of third party image processing software
  • Easy access to all data with plotting functions
  • Integrates seamlessly with R statistics
  • Configurable data processing functions
  • Visualisation of data and images
  • Report generator
  • Database management on server or PC
  • Open access to databases with full documentation
  • Graphical display of images, data and analysis
  • Location data for plants and sensors