ROSE-X: an annotated data set for evaluation of 3D plant organ segmentation methods

Plant Methods
Helin DutagaciDavid Rousseau

Abstract

The production and availability of annotated data sets are indispensable for training and evaluation of automatic phenotyping methods. The need for complete 3D models of real plants with organ-level labeling is even more pronounced due to the advances in 3D vision-based phenotyping techniques and the difficulty of full annotation of the intricate 3D plant structure. We introduce the ROSE-X data set of 11 annotated 3D models of real rosebush plants acquired through X-ray tomography and presented both in volumetric form and as point clouds. The annotation is performed manually to provide ground truth data in the form of organ labels for the voxels corresponding to the plant shoot. This data set is constructed to serve both as training data for supervised learning methods performing organ-level segmentation and as a benchmark to evaluate their performance. The rosebush models in the data set are of high quality and complex architecture with organs frequently touching each other posing a challenge for the current plant organ segmentation methods. We report leaf/stem segmentation results obtained using four baseline methods. The best performance is achieved by the volumetric approach where local features are trained with a random fo...Continue Reading

References

Mar 4, 2005·IEEE Transactions on Pattern Analysis and Machine Intelligence·Yuri Boykov, Vladimir Kolmogorov
May 5, 2012·BMC Plant Biology·Anthony PaprokiJurgen Fripp
Oct 11, 2013·Plant Methods·Guillaume LobetClaire Périlleux
Feb 19, 2014·Sensors·Stefan PaulusHeiner Kuhlmann
Aug 9, 2015·BMC Bioinformatics·Mirwaes WahabzadaAnne-Katrin Mahlein
May 3, 2016·Sensors·Manuel Vázquez-ArellanoDimitris S Paraforos
Oct 20, 2017·GigaScience·Fernando Perez-SanzMarcos Egea-Cortines
Jan 30, 2018·Plant Methods·Julio V SchneiderJörg Habersetzer
Jul 23, 2018·Current Opinion in Biotechnology·Jonathan A AtkinsonDarren M Wells

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Methods Mentioned

BETA
X-ray
feature extraction

Software Mentioned

ilastik
MATLAB
Net
Python
LFVD
LFPC

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