Publication Details |
| Category | Text Publication |
| Reference Category | Journals |
| DOI | 10.1186/s13007-021-00735-4 |
Licence  |
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| Title (Primary) | An improved method for the segmentation of roots from X-ray computed tomography 3D images: Rootine v.2 |
| Author | Phalempin, M.; Lippold, E.; Vetterlein, D.; Schlüter, S. |
| Source Titel | Plant Methods |
| Year | 2021 |
| Department | BOSYS |
| Volume | 17 |
| Page From | art. 39 |
| Language | englisch |
| Topic | T5 Future Landscapes |
| Keywords | High-throughput root phenotyping; Image analysis; Root segmentation; Root system architecture; Cylindrical feature detection; X-ray computed tomography; Root diameter |
| Abstract | Background X-ray computed tomography is acknowledged as a powerful tool
for the study of root system architecture of plants growing in soil. In
this paper, we improved the original root segmentation algorithm
"Rootine" and present its succeeding version "Rootine v.2". In addition
to gray value information, Rootine algorithms are based on shape
detection of cylindrical roots. Both algorithms are macros for the
ImageJ software and are made freely available to the public. New
features in Rootine v.2 are (i) a pot wall detection and removal step to
avoid segmentation artefacts for roots growing along the pot wall, (ii)
a calculation of the root average gray value based on a histogram
analysis, (iii) an automatic calculation of thresholds for hysteresis
thresholding of the tubeness image to reduce the number of parameters
and (iv) a false negatives recovery based on shape criteria to increase
root recovery. We compare the segmentation results of Rootine v.1 and
Rootine v.2 with the results of root washing and subsequent analysis
with WinRhizo. We use a benchmark dataset of maize roots (Zea mays L.
cv. B73) grown in repacked soil for two scenarios with differing soil
heterogeneity and image quality. Results We demonstrate that Rootine v.2 outperforms its preceding version in terms of root recovery and enables to match better the root diameter distribution data obtained with root washing. Despite a longer processing time, Rootine v.2 comprises less user-defined parameters and shows an overall greater usability. Conclusion The proposed method facilitates higher root detection accuracy than its predecessor and has the potential for improving high-throughput root phenotyping procedures based on X-ray computed tomography data analysis. |
| Persistent UFZ Identifier | https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=24576 |
| Phalempin, M., Lippold, E., Vetterlein, D., Schlüter, S. (2021): An improved method for the segmentation of roots from X-ray computed tomography 3D images: Rootine v.2 Plant Methods 17 , art. 39 10.1186/s13007-021-00735-4 |
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