Phenotyping studies require robust statistics, and high sample numbers are key to provide a solid data base. Thus, automatic handling strongly supports the image and data acquisition in high throughput solutions. Thereby, either sensing equipment moves towards the samples (sensor-to-plant), or the plants are transported towards the cameras (plant-to-sensor). Plant-to-sensor allows optimised image acquisition conditions in dedicated cabinets with top-and-side view, but demands for moving the plants. Sensor-to-plant keeps the plants at their place, and top-view imaging equipment passes by the growing area.
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Software for Experiment Control and Image Processing
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.
Schematic representation of the mode of operation.
Illustration of software modules for data acquisition, processing, management and analysis operated on dedicated computer hardware.
Please click on the image for a larger view.
The LemnaTec software consists of the following modules that serve for the tasks
as described above:
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.
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.
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.
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.
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.