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

Abstract

Background and aims. 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 intensive 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. Methods and results. rhizoTrak builds on TrakEM2 and is publically 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 conflicts. It facilitates easy data exchange with other software by supporting open data formats. Conclusions. 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.

First estimates of fine root production in tropical peat swamp and terra firme forests of the central Congo Basin

“…Image quality was then improved employing Adobe Lightroom. Lastly, changes in root length between consecutive pairs of images were analysed operating rhizoTrak, open-source software designed to analyse root length in minirhizotron images 46 , see Fig. 1 .…”

Ecotrons: Powerful and versatile ecosystem analysers for ecology, agronomy and environmental science

“…Other ecotrons focus on automatic measurements of ecosystem properties that are not related to ecosystem gas exchange. These include root growth using minirhizotrons (Möller et al, 2019), invertebrate and plant community composition using novel imaging techniques like computerized trap systems, video cameras or radio frequency identification (Dell et al, 2014; Dombos et al, 2017), thermography to analyse the heterogeneity of transpiration, and hyperspectral reflectance for canopy biomass and chemical content (Tan et al, 2018; Xie et al, 2020). Similar to what is done in other experimental settings, in all ecotron experiments the automatic measurements are complemented by low‐frequency samplings of soil, plants, soil solution, leachate, etc., for further analysis of fauna and microbe diversity, elemental and isotopic composition of soil, water and plant material, delivering a more complete understanding of the impact of the experimental treatments.…”

The iDiv Ecotron—A flexible research platform for multitrophic biodiversity research

“…In this way, up to 96 subunits with various biotic and abiotic variables to be manipulated and measured independently can be set up. The iDiv Ecotron concept was developed in cooperation with numerous scientists and technicians from iDiv, including strong participation by the UFZ, national and international collaborators, and the companies "EMC -Gesellschaft zur Erfassung und Bewertung von Umweltdaten mbH," and "Umwelt-Geräte-Technik GmbH (UGT), the sensors offer the opportunity to install minirhizotrons (acrylic glass tubes) for horizontal monitoring of root development using a portable root scanner (see Möller et al, 2019).…”