LemnaTec Phenotyping Software
The core of all LemnaTec phenotyping 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.
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. 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):
|Sensor||Recorded parameters||Information to derive from parameters|
|Visible light camera||Reflectance 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 light||Presence and distributions of fluorescencent pigments; stress and senescence|
|Camera for chlorophyll fluorescence dynamics (Kautsky/PAM)||Photosystem II-related parameters||Photosynthetic capacity and activity; stress, pathogen responses|
|NIR camera with 1450 nm filter||Water-content related NIR signal||Tissue moisture; water stress responses|
|IR camera||Surface heat emission||Plant temperatures, transpiration|
|Hyper-/multispectral camera||Spectrally resolved reflectance||Physiological parameters, vegetation indices|
|Laser scanner||Point clouds||3D 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 Scanalyzer systems 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.
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 e.g. germination features.
Data Analysis and visualisation:
The LemnaExplorer software allows visualization of the all experiment-related data in the data base. Dedicated filtering allows fast sub setting of data and outlier detection. The organization into experiment-specific dashboards allows custom-made data aggregation, processing and visualization.
The LemnaExplorer software is a web-based tool (i.e. it runs in the browser) and can hence be widely accessed within the customers network, allowing flexible exploration of the data set.
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.