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3D reconstruction using Structure-from-Motion: a new technique for morphological measurement of tree root systems



Clarification of root architecture is important for understanding tree root functions. 3D laser scanning reconstructs the 3D structure of root system with high accuracy, but the devices are large and expensive. The Structure-from-Motion with multi-view stereo-photogrammetry (SfM-MVS) method reconstructs the 3D structure of an object from multiple images. This method is suitable for field research because it acquires the 3D data with a commercially available digital camera. Our aim in this study was to test the applicability of the SfM-MVS method for morphological measurement of tree root systems.


The 3D root system model was created using a dummy and three black pine (Pinus thunbergii) root systems. Image data were collected from the root systems using a camera and reconstructed using the free software, VisualSfM and MeshLab. We evaluated the accuracy of morphological data estimated from the 3D models by comparing them with real data obtained from manual measurements of the root systems.


The 3D reconstructions of the dummy and black pine root systems were successful. The root mean squared error values for the morphological features in the pine root systems ranged from 4 to 24%, which was sufficiently accurate for a successful 3D model. However, the RMSE values were larger than that of dummy root, ranging from 2 to 9%.


The SfM-MVS method is a new tool, based on non-specialised equipment and free software, to obtain the 3D structure of tree root systems. The morphological features of it can be successfully measured from the reconstructed models.

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Availability of data and material

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Code availability

Not applicable.


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We thank Mr. Shigetomo Ohashi (Manbokuen), for their invaluable field assistance. We also thank the Aichi Prefecture Fisheries Center, Aichi Prefectural Government, Tahara City Government for permission to use the field site. We further thank Dr. Toshifumi Kimura for internally reviewed. We thank Dr. Leonie Seabrook from Edanz Co., Ltd. for editing English of a draft of this manuscript.


This study was partly supported by JSPS KAKENHI Grants no. JP20H03040, JP20H03028, JP18H02243, JP20KK0241, by JSPS Bilateral Program Grants no. JPJSBP120209933 and by the 28th and 29th Botanical Research Grants of ICHIMURA Foundation for New Technology.

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Yuki Okamoto and Hidetoshi Ikeno conceived the research idea; all authors collected the data; Yuki Okamoto performed statistical analyses; Yuki Okamoto, with contributions from Mizue Ohashi and Hidetoshi Ikeno, wrote the paper; all authors discussed the results and commented on the manuscript.

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Correspondence to Yuki Okamoto.

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Supplementary Information

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Supplementary file2 (MP4 3461 kb) Online Resource 2 The 3D model of black pine Root B produced using SfM-MVS.


Supplementary file1 (PPTX 40 kb) Online Resource 1 The drawing of the dummy root system. This is made of five long horizontal roots (A to E), five short horizontal roots (F to J), and one vertical root (K). The length of A-E, F-J and K were 0.75 to 0.85, 0.40 to 0.45 and 0.5 m respectively. The diameter of A-E, F-J and K were 20 to 40, 20 to 40 and 150 mm, respectively.


Supplementary file3 (PPTX 820 kb) Online Resource 3 The complete 3D model (a) and three incomplete 3D models (b, c and d) of Roots A made by SfM-MVS. In the case of (c), a part of the root system was wrongly reproduced above the stump.


Supplementary file4 (PPTX 207 kb) Online Resource 4 Regression analysis of the data from actual and SfM-MVS measurements in the three black pine root systems (Roots A, B and C). (a)-(c), (d)-(f) and (g)-(i) are the diameter, length, and angle, respectively. The dotted line shows the slope of 1.00.

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Okamoto, Y., Ikeno, H., Hirano, Y. et al. 3D reconstruction using Structure-from-Motion: a new technique for morphological measurement of tree root systems. Plant Soil (2022).

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  • 3D model
  • SfM-MVS
  • Root system architecture
  • Morphometry
  • VisualSfM
  • MeshLab