RootAIxpert HT

The automated root- and shoot- phenotyping systems for plants growing in large rhizotrons

RootAIxpert HT is an automated root- and shoot-phenotyping system for plants grown in flat rhizotrons that are stored in magazine rows. RootAIxpert HT is the root-oriented phenotyping system that enables growth in soil environments at optimal root visibility. With the possibility to use large rhizotrons, it provides substantial soil bodies for root growth. Automation for imaging and weighing/watering allows handling large sample numbers, facilitating advanced statistics. Rhizotrons are stored at an angle of 45° to maximize the fraction of visible roots at the transparent plate. With an imaging cabinet moving along the magazine, phenotypic measurements can be done automatically at high throughput. Handling large numbers of rhizotrons in repeated measurements, the system enables advanced statistical analyses and comparisons across genotype- and treatment-groups at root- and shoot- levels. Systems are customized according to the customers’ measuring demand and edificial conditions1.

RootAIxpert HT

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Features

  • Simultaneous phenotyping of root and shoot

  • Phenotyping software for comprehensive trait analysis

  • Machine learning available for complex traits

  • High resolution visible light imaging of root system

  • Horizontal and vertical visible light imaging of shoot system

  • Rhizotrons in magazine rows

  • Imaging cabinet moves along magazine

  • Automatic rhizotron loading for imaging

  • Rhizotron weighing and watering

  • Optional supply of liquid fertilizer2

Download the “RootAIxpert HT” product brochure as a PDF document.

1 A technical feasibility check is required before installation.
2 Chemical properties of liquids must be compatible with the technical equipment

RootAIxpert HT applications in research and development

The root- and shoot- imaging options in RootAIxpert HT, combined with the comprehensive capabilities of image analysis in the corresponding LemnaTec software package enables several applications in research, product development, or monitoring. As a unique feature, the system allows monitoring roots and shoots of individual plants in one working step and as time-resolved measuring series. Typical application cases are:

  • Root-shoot-relations in plant development

  • Root interactions with other plants, or with soil environment

  • Studies on growth and development

  • Genotype-phenotype relations

  • Genetic screening

  • Treatment screening

  • Environmental responses and climate adaptation

  • Stress- and disease assessments

Technical features

The system consists of magazine rows for rhizotrons and imaging cabinets that move along the magazine and take the rhizotrons inside for image recording and weighing/watering. A system can consist of one or more magazine rows. A moving imaging cabinet can operate one or two (left and right of the moving direction) magazine rows.

  • Soil-filled rhizotrons in magazines at 45° angle

  • Roots grow along transparent plate, shoots grow above the box

  • One or multiple rows of rhizotrons

  • Imaging cabinet moves along the row and drags in rhizotrons for imaging

  • Minimum 12 Megapixel industrial cameras

  • Imaging inside the box with root- and shoot directed cameras combined with customized illumination

  • Rhizotron weighing and supply of water and fertilizer combined with the imaging process

  • Database for plant data and metadata

  • Software package for system control, data recording, and image analysis

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Phenotypic trait analysis includes

Phenotyping software enables extracting traits from images, for roots as well as for shoots. The parameters derived from images can be interpreted for biological functions and properties.

  • Root- and shoot length and area

  • Length and width of root system and shoot system

  • Morphological factors of root system and shoot system

  • Color features of shoots and leaves

  • Root system architecture

  • Rooting depth

  • Root density per soil layer

Imaging and image processing example of a root system grown in a rhizotron – Root system dimensions and morphology, root branching and angels, rooting depth and root density per soil layer.

Software Suite

The RootAIxpert HT is delivered with a comprehensive software suite. The software enables the users to provide sample information and control cameras and lights. After imaging all data are stored and accessible for image and data processing. LemnaControl is the interface with which users operate the system. With LemnaControl, users carry out all settings that are required for image recording with the system. In particular, his comprises settings for the camera(s) and lights included in the system. All settings can be combined and scheduled to configure recordings. The available functions are tailored to the corresponding hardware. Each hardware system delivered by LemnaTec comes with its own control software adapted for the functions of that system. The LemnaGrid app uses an intuitive graphical programming environment, which allows for easy integration of different image analysis algorithms. LemnaGrid phenotyping software offers high flexibility for user programming. The image processing pipeline extracts desired properties/features from the original image and stores results in a dedicated storage system. LemnaGrid can include functions of state-of-the-art machine learning tools, next to standard image analysis to detect and extract features of interest. Guided by the LemnaGrid graphical user interface, users can build their own analytical pipeline with pre-defined devices.

Analysis devices include:

  • filters
  • threshold functions
  • image converters
  • object detectors
  • feature detectors
  • color analysis tools
  • region of interest function
  • combinatory functions
  • and many more

All devices – graphically represented by boxes – can be combined on a interface by aligning the boxes to pipelines. Along such workflows, each function can provide insights in the progress of the analysis by feeding out an intermediate image. Image processing pipelines can include branches and parallel paths that combine to a final result. For 3D data, the app Lemna3D is used for programming analytical pipelines. Similarly as in LemnaGrid, users can do graphical programming on an interface by combining devices from a library of functions.

LemnaExperiment serves to manage experiments and measurements, and to schedule and run analyses. Moreover, it enables viewing, visualizing, and exporting results. It provides capabilities to access and browse through recorded images and to display metadata for samples and measurements. As core function, LemnaExperiment selects recordings for analysis and assigns an image analysis pipeline –written in LemnaGrid or in Lemna3D – to a given set of recordings. After assignment, the analyses are run in the background by the Analysis Executor. Parameters of interest can be selected in LemnaExperiment so that they are displayed in the analysis output.

LemnaTec Product Matrix

LemnaTec offers imaging and image processing technologies for several applications that suit for low to high throughput in laboratory, greenhouse or outdoor environments. Technologies are adapted to various sample types and can be combined with automation. All imaging systems are combined with dedicated image processing software, including user-programmable functions and machine learning.