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

  • Birgit MöllerEmail author
  • Hongmei ChenEmail author
  • Tino Schmidt
  • Axel Zieschank
  • Roman Patzak
  • Manfred Türke
  • Alexandra Weigelt
  • Stefan Posch
Methods Paper

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 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.

Methods and results

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.

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.

Keywords

minirhizotron images Time-series Manual annotation Open source Free Platform-independent 

Notes

Acknowledgements

We are grateful to Nico Eisenhauer and Georg Mathias for their support to develop this software via the iDiv Ecotron platform. In addition, we thank Berit Schreck for her support in software development and testing, and Lisa Ertel for experimentally evaluating rhizoTrak.

Funding

H. Chen was funded by the German Science Foundation (DFG, Jena Experiment research group FOR 1451). M. Türke, T. Schmidt and A. Zieschank were co-funded by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (DFG FZT 118) and by the Helmholtz Association in the framework of the iDiv Ecotron research platform.

Compliance with Ethical Standards

Conflict of interests

The authors declare that they have no conflict of interest.

Supplementary material

11104_2019_4199_MOESM1_ESM.pdf (1.7 mb)
(PDF 1.67 MB)
11104_2019_4199_MOESM2_ESM.csv (521 kb)
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11104_2019_4199_MOESM3_ESM.csv (2 kb)
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11104_2019_4199_MOESM4_ESM.pdf (56 kb)
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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Institute of Computer ScienceMartin Luther University Halle-WittenbergHalle (Saale)Germany
  2. 2.Institute of BiologyLeipzig UniversityLeipzigGermany
  3. 3.German Center of Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzigGermany
  4. 4.Institute of Biological and Medical ImagingHelmholtz Zentrum München - German Research Center for Environmental HealthNeuherbergGermany

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