rhizoTrak: a flexible open source Fiji plugin for user-friendly manual annotation of time-series images from minirhizotrons

Minirhizotrons are commonly used to study root turnover which is essential for understanding ecosystem carbon and nutrient cycling. Yet, extracting data from minirhizotron images requires extensive annotation effort. Existing annotation tools often lack flexibility and provide only a subset of the required functionality. To facilitate efficient root annotation in minirhizotrons, we present the user-friendly open source tool rhizoTrak. rhizoTrak builds on TrakEM2 and is publicly available as Fiji plugin. It uses treelines to represent branching structures in roots and assigns customizable status labels per root segment. rhizoTrak offers configuration options for visualization and various functions for root annotation mostly accessible via keyboard shortcuts. rhizoTrak allows time-series data import and particularly supports easy handling and annotation of time-series images. This is facilitated via explicit temporal links (connectors) between roots which are automatically generated when copying annotations from one image to the next. rhizoTrak includes automatic consistency checks and guided procedures for resolving inconsistencies. It facilitates easy data exchange with other software by supporting open data formats. rhizoTrak covers the full range of functions required for user-friendly and efficient annotation of time-series images. Its flexibility and open source nature will foster efficient data acquisition procedures in root studies using minirhizotrons.

• Publication year

  2019

• Venue

  Plant and Soil

• Publication date

  2019-02-13

• Fields of study

  Biology, Computer Science, Environmental Science

• Identifiers
  DOI 10.1007/s11104-019-04199-3
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions

  2017influential reference
• GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

  2015cited by this paper
• Root System Markup Language: Toward a Unified Root Architecture Description Language1[OPEN]

  2015influential reference
• Next generation shovelomics: set up a tent and REST

  2015cited by this paper
• Redefining fine roots improves understanding of below-ground contributions to terrestrial biosphere processes.

  2015cited by this paper
• R: A language and environment for statistical computing.

  2014cited by this paper
• RootNav: Navigating Images of Complex Root Architectures1[C][W]

  2013cited by this paper
• Biomass allocation to leaves, stems and roots: meta-analyses of interspecific variation and environmental control.

  2012cited by this paper
• Root taxa identification in plant mixtures – current techniques and future challenges

  2012cited by this paper
• TrakEM2 Software for Neural Circuit Reconstruction

  2012influential reference
• Fiji: an open-source platform for biological-image analysis

  2012influential reference
• Fine Root Turnover

  2012cited by this paper
• Minirhizotrons in Modern Root Studies

  2012cited by this paper
• GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons.

  2012cited by this paper
• A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture1[W][OA]

  2011cited by this paper
• Rapid automated detection of roots in minirhizotron images

  2010cited by this paper
• DART: a software to analyse root system architecture and development from captured images

  2009cited by this paper
• A region and contour based technique for automatic detection of tomato roots in minirhizotron images

  2005cited by this paper
• Root Ecology

  2003cited by this paper
• Advancing fine root research with minirhizotrons.

  2001cited by this paper
• Root methods: A handbook

  2000influential reference
• Global patterns of root turnover for terrestrial ecosystems

  2000cited by this paper
• Root Methods

  2000cited by this paper
• A global budget for fine root biomass, surface area, and nutrient contents.

  1997cited by this paper
• Root sampling methods - applications and limitations of the minirhizotron technique

  1996cited by this paper
• THE DEMOGRAPHY OF FINE ROOTS IN A NORTHERN HARDWOOD FOREST

  1992cited by this paper
• A New Biometrical Procedure for Testing the Equality of Measurements from Two Different Analytical Methods. Application of linear regression procedures for method comparison studies in Clinical Chemistry, Part I

  1983cited by this paper

• Crop root system phenotyping with high water-use efficiency and its targeted precision regulation: Present and prospect

  2025cites this paper
• faCRSA: an automated pipeline for high-throughput analysis of crop root system architecture

  2025cites this paper
• Single-time fertilization of controlled release blended fertilizer optimizes soil nitrogen distribution and root characteristics to increase conventional japonica rice (Oryza sativa L.) grain yield and nitrogen use efficiency

  2025cites this paper
• Recurrent summer drought temporarily stimulates fine root growth but enhances winter root losses in alpine grassland

  2025cites this paper
• One-time application of controlled-release blended fertilizer increases rice yield and nitrogen utilization by optimizing root morphological trait distribution and nitrogen uptake

  2025cites this paper
• Hydrology mediates salt marsh belowground biomass response to warming

  2025cites this paper
• Optimizing the Scale of Spatial Aggregation in Minirhizotron Studies of Crop Root System Distribution

  2025cites this paper
• Multi-year belowground data of minirhizotron facilities in Selhausen

  2023cites this paper
• First estimates of fine root production in tropical peat swamp and terra firme forests of the central Congo Basin

  2023cites this paper
• Semantic segmentation of plant roots from RGB (mini-) rhizotron images—generalisation potential and false positives of established methods and advanced deep-learning models

  2023cites this paper
• Four-dimensional measurement of root system development using time-series three-dimensional volumetric data analysis by backward prediction

  2022cites this paper
• Growth of alpine grassland will start and stop earlier under climate warming

  2022cites this paper
• Recent advances in methods for in situ root phenotyping

  2022cites this paper
• Development and Validation of a Deep Learning Based Automated Minirhizotron Image Analysis Pipeline

  2022cites this paper
• Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

  2022cites this paper
• The iDiv Ecotron—A flexible research platform for multitrophic biodiversity research

  2021cites this paper
• Ecotrons: Powerful and versatile ecosystem analysers for ecology, agronomy and environmental science

  2020cites this paper
• Overcoming Small Minirhizotron Datasets Using Transfer Learning

  2019cites this paper