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 News
rhizoTrak features
- 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
- functions to propagate diameter and status information of treelines to connected
treelines in subsequent layers
- 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
- an optional user-configurable scalebar
- 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
rhizoTrak includes:
- the R rhizoTrakAddons package to assist in analyzing and processing csv files generated by rhizoTrak
Sample image and annotation
rhizoTrak is developed
Imprint
