rhizoTrak

Martin Luther University Halle-Wittenberg and Leipzig University

Overview

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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Description

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