Non-destructive 3D geometric modeling of maize root-stubble in-situ via X-ray computed tomography
Keywords:
maize root-stubble, non-destructive modeling, X-ray computed tomography, variational level set methodAbstract
No-tillage seeding has become an important approach to improve crop productivity, which needs colters of high performance to cut the root-stubble-soil composite. However, the difficulty of maize root-stubbles three-dimensional (3D) modeling hinders finite element (FE) simulation to improve development efficiency of such colters because of maize root system complexity and opaque nature of the soil. Fortunately, the non-destructive 3D geometric model of the maize root-stubble in-situ can be established via X-ray computed tomography (CT) following by a systematic procedure. The whole procedure includes CT scanning of the maize root-stubble-soil composite sample, image reconstruction via filtered back-projection (FBP) with the Hanning filter, segmentation of root-stubble via a variational level set method, and post-processing via morphological operations. The 3D reconstruction model of the maize root-stubble in-situ presents a complete, complex and in-situ geometrical morphology, which cannot be realized via other methods, including the destructive modelling after washing via CT. This study is the first to build a 3D geometric model of a maize root-stubble in-situ via CT, which opens up new possibilities for simulation of root-stubble-soil cutting using FEM, and much other research related to plant root-stubbles. Keywords: maize root-stubble, non-destructive modeling, X-ray computed tomography, variational level set method DOI: 10.25165/j.ijabe.20201303.5268 Citation: Zhao X, Xing L Y, Shen S F, Liu J M, Zhang D X. Non-destructive 3D geometric modeling of maize root-stubble in-situ via X-ray computed tomography. Int J Agric & Biol Eng, 2020; 13(3): 174–179.References
[1] Zeng, Z W, Chen Y. The performance of a fluted coulter for vertical tillage as affected by working speed. Soil and Tillage Research, 2018; 175: 112–118.
[2] Upadhyaya S K., Rosa U A., Wulfsohn D. Application of the finite element method in agricultural soil mechanics. Advances in Soil Dynamics, 2002; 2: 117–153.
[3] Li M, Xu S, Yang Y W, Guo L, Tong J. A 3D simulation model of corn stubble cutting using finite element method. Soil and Tillage Research, 2017; 166: 43–51.
[4] Mairhofer S, Sturrock C, Wells D M., Bennett M J, Mooney S J, Pridmore T P. On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images. Functional Plant Biology, 2015; 42(5): 460.
[5] Mooney S J, Morris C, Berry P M. Visualization and quantification of the effects of cereal root lodging on three-dimensional soil macrostructure using X-ray computed tomography. Soil science, 2006; 171(9): 706–718.
[6] Kaestner A, Schneebeli M, Graf F. Visualizing three-dimensional root networks using computed tomography. Geoderma, 2006; 136(1-2): 459–469.
[7] Lontoc-Roy M, Dutilleul P, Prasher S O, Han L, Brouillet T, Smith D L. Advances in the acquisition and analysis of CT scan data to isolate a crop root system from the soil medium and quantify root system complexity in 3-D space. Geoderma, 2006; 137(1-2): 231–241.
[8] Perret J S, Al-Belushi M E, Deadman M. Non-destructive visualization and quantification of roots using computed tomography. Soil Biology and Biochemistry, 2007; 39(2): 391–399.
[9] Han L, Dutilleul P, Prasher S O, Beaulieu C, Smith D L. Assessment of density effects of the common scab-inducing pathogen on the seed and peripheral organs of potato during growth using computed tomography scanning data. Transactions of the ASABE, 2009; 52(1): 305–311.
[10] Hargreaves C E, Gregory P J, Bengough A G. Measuring root traits in barley (Hordeum vulgare ssp. vulgare and ssp. spontaneum) seedlings using gel chambers, soil sacs and X-ray microtomography. Plant and Soil, 2009; 316(1-2): 285–297.
[11] Mairhofer S, Zappala S, Tracy S, Sturrock C, Bennett M. J, Mooney S. J, et al. Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography. Plant Methods, 2013; 9(1): 8.
[12] Koebernick N, Weller U, Huber K, Schlüter S, Vogel H J, Jahn R, et al. In situ visualization and quantification of three-dimensional root system architecture and growth using X-ray computed tomography. Vadose Zone Journal, 2014; 13(8).
[13] Xu Z, Valdes C, Clarke J. Existing and potential statistical and computational approaches for the analysis of 3D CT images of plant roots. Agronomy, 2018; 8(5): 71.
[14] Tabb A, Duncan K E, Topp C N. Segmenting root systems in X-ray computed tomography images using level sets. In: 2018 IEEE Winter Conference on Applications of Computer Vision (WACV), Lake Tahoe: IEEE. 2018. pp. 586–595.
[15] Maenhout P, Sleutel S, Xu H, Van Hoorebeke L, Cnudde V, De Neve S. Semi-automated segmentation and visualization of complex undisturbed root systems with X-ray μCT. Soil and Tillage Research, 2019; 192: 59–65.
[16] Zheng X, Valdes C, Clarke J. Existing and potential statistical and computational approaches for the analysis of 3D CT images of plant roots. Agronomy, 2018; 8(5): 71.
[17] Kalender W A. Computed tomography: Fundamentals, system technology, image quality, applications. John Wiley & Sons, 2011. 372 p.
[18] Li J Y, Jaszczak R J, Coleman R E. A filtered backprojection algorithm for axial head motion correction in fan-beam SPECT. Physics in Medicine and Biology, 1995; 40(12): 2053–2063.
[19] Li C M, Kao C Y, Gore J C, Ding Z H. Minimization of region-scalable fitting energy for image segmentation. IEEE transactions on image processing, 2008; 17(10): 1940–1949.
[20] Gonzalez R C, Woods R E, Eddins S L. Digital Image Processing Using MATLAB, 2nd Edition. Gatesmark Publishing, 2010; 827 p.
[2] Upadhyaya S K., Rosa U A., Wulfsohn D. Application of the finite element method in agricultural soil mechanics. Advances in Soil Dynamics, 2002; 2: 117–153.
[3] Li M, Xu S, Yang Y W, Guo L, Tong J. A 3D simulation model of corn stubble cutting using finite element method. Soil and Tillage Research, 2017; 166: 43–51.
[4] Mairhofer S, Sturrock C, Wells D M., Bennett M J, Mooney S J, Pridmore T P. On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images. Functional Plant Biology, 2015; 42(5): 460.
[5] Mooney S J, Morris C, Berry P M. Visualization and quantification of the effects of cereal root lodging on three-dimensional soil macrostructure using X-ray computed tomography. Soil science, 2006; 171(9): 706–718.
[6] Kaestner A, Schneebeli M, Graf F. Visualizing three-dimensional root networks using computed tomography. Geoderma, 2006; 136(1-2): 459–469.
[7] Lontoc-Roy M, Dutilleul P, Prasher S O, Han L, Brouillet T, Smith D L. Advances in the acquisition and analysis of CT scan data to isolate a crop root system from the soil medium and quantify root system complexity in 3-D space. Geoderma, 2006; 137(1-2): 231–241.
[8] Perret J S, Al-Belushi M E, Deadman M. Non-destructive visualization and quantification of roots using computed tomography. Soil Biology and Biochemistry, 2007; 39(2): 391–399.
[9] Han L, Dutilleul P, Prasher S O, Beaulieu C, Smith D L. Assessment of density effects of the common scab-inducing pathogen on the seed and peripheral organs of potato during growth using computed tomography scanning data. Transactions of the ASABE, 2009; 52(1): 305–311.
[10] Hargreaves C E, Gregory P J, Bengough A G. Measuring root traits in barley (Hordeum vulgare ssp. vulgare and ssp. spontaneum) seedlings using gel chambers, soil sacs and X-ray microtomography. Plant and Soil, 2009; 316(1-2): 285–297.
[11] Mairhofer S, Zappala S, Tracy S, Sturrock C, Bennett M. J, Mooney S. J, et al. Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography. Plant Methods, 2013; 9(1): 8.
[12] Koebernick N, Weller U, Huber K, Schlüter S, Vogel H J, Jahn R, et al. In situ visualization and quantification of three-dimensional root system architecture and growth using X-ray computed tomography. Vadose Zone Journal, 2014; 13(8).
[13] Xu Z, Valdes C, Clarke J. Existing and potential statistical and computational approaches for the analysis of 3D CT images of plant roots. Agronomy, 2018; 8(5): 71.
[14] Tabb A, Duncan K E, Topp C N. Segmenting root systems in X-ray computed tomography images using level sets. In: 2018 IEEE Winter Conference on Applications of Computer Vision (WACV), Lake Tahoe: IEEE. 2018. pp. 586–595.
[15] Maenhout P, Sleutel S, Xu H, Van Hoorebeke L, Cnudde V, De Neve S. Semi-automated segmentation and visualization of complex undisturbed root systems with X-ray μCT. Soil and Tillage Research, 2019; 192: 59–65.
[16] Zheng X, Valdes C, Clarke J. Existing and potential statistical and computational approaches for the analysis of 3D CT images of plant roots. Agronomy, 2018; 8(5): 71.
[17] Kalender W A. Computed tomography: Fundamentals, system technology, image quality, applications. John Wiley & Sons, 2011. 372 p.
[18] Li J Y, Jaszczak R J, Coleman R E. A filtered backprojection algorithm for axial head motion correction in fan-beam SPECT. Physics in Medicine and Biology, 1995; 40(12): 2053–2063.
[19] Li C M, Kao C Y, Gore J C, Ding Z H. Minimization of region-scalable fitting energy for image segmentation. IEEE transactions on image processing, 2008; 17(10): 1940–1949.
[20] Gonzalez R C, Woods R E, Eddins S L. Digital Image Processing Using MATLAB, 2nd Edition. Gatesmark Publishing, 2010; 827 p.
Downloads
Published
2020-06-08
How to Cite
Zhao, X., Xing, L., Shen, S., Liu, J., & Zhang, D. (2020). Non-destructive 3D geometric modeling of maize root-stubble in-situ via X-ray computed tomography. International Journal of Agricultural and Biological Engineering, 13(3), 174–179. Retrieved from https://ijabe.migration.pkpps03.publicknowledgeproject.org/index.php/ijabe/article/view/5268
Issue
Section
Information Technology, Sensors and Control Systems
License
IJABE is an international peer reviewed open access journal, adopting Creative Commons Copyright Notices as follows.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
