Martin Luther University Halle-Wittenberg and Leipzig University


Measured variables length, diameter, topology
Operating system windows, mac, linux
Licence open-source, freeware
Automation level manual
Plant requirements any
Export formats rsml, csv
Other information Works as a FIJI plugin

Scientific article(s)

rhizoTrak: A flexible open source Fiji plugin for user-friendly manual annotation of time-series images from minirhizotrons
Birgit Moeller,Hongmei Chen,Tino Schmidt,Axel Zieschank,Roman Patzak,Manfred Tuerke,Alexandra Weigelt,Stefan Posch
biorXiv, 2019 View paper

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rhizoTrak is:

  • an open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images
  • building on TrakEM2,
  • realized as a Fiji plugin available for Windows, Linux, and MacOS.
rhizoTrak supports:
  • import and processing of the complete set of images of a time series in one single project
  • easy browsing through time points which enables to annotate roots by simultaneously considering images of different time points
  • temporal links between roots in different images which explicitly represented identity of the same physical root via so-called connectors
  • easy transfer of annotation data of one time point to the next as initial annotation where connectors between corresponding root annotations are automatically established
  • automatic checks for inconsistencies in root typology due to merging of roots and assistance in solving them
  • the inherent representation of branching roots by modeling roots as treelines
  • an individual radius for each node of a treeline, and user-definable status labels for segments of treelines
  • a large collection of editing operations for root treelines including split and merge, where many of these operations are easily accessible via keyboard shortcuts
  • different visualization options for treelines and fast hiding and un-hiding of all annotated treelines
  • redirection of treelines which is important as the upstream and downstream of a root is often not straightforward to be identified in minirhizotron images
  • import and export of annotations from/to RSML format,
  • export of root measurements in a tab-separated format including the option to aggregate measurements within images
  • a plugin mechanism to merge results from automatic segmentation method which are to be implemented as a MiToBo operator

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