journal article·2024-04-16Open access

A Novel Method Combining U-Net with LSTM for Three-Dimensional Soil Pore Segmentation Based on Computed Tomography Images

Lei Liu, Qiaoling Han, Yue Zhao, Yandong Zhao

Applied Sciences· Volume 14· Issue 8

Abstract

The non-destructive study of soil micromorphology via computed tomography (CT) imaging has yielded significant insights into the three-dimensional configuration of soil pores. Precise pore analysis is contingent on the accurate transformation of CT images into binary image representations. Notably, segmentation of 2D CT images frequently harbors inaccuracies. This paper introduces a novel three-dimensional pore segmentation method, BDULSTM, which integrates U-Net with convolutional long short-term memory (CLSTM) networks to harness sequence data from CT images and enhance the precision of pore segmentation. The BDULSTM method employs an encoder–decoder framework to holistically extract image features, utilizing skip connections to further refine the segmentation accuracy of soil structure. Specifically, the CLSTM component, critical for analyzing sequential information in soil CT images, is strategically positioned at the juncture of the encoder and decoder within the U-shaped network architecture. The validation of our method confirms its efficacy in advancing the accuracy of soil pore segmentation beyond that of previous deep learning techniques, such as U-Net and CLSTM independently. Indeed, BDULSTM exhibits superior segmentation capabilities across a diverse array of soil conditions. In summary, BDULSTM represents a state-of-the-art artificial intelligence technology for the 3D segmentation of soil pores and offers a promising tool for analyzing pore structure and soil quality.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Advanced Neural Network Applications · AI in cancer detection · Soil and Unsaturated Flow

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

School of Technology, Beijing Forestry University, Beijing 100083, China

Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Municipal Education Commission, Beijing 100083, China

Key Laboratory of State Forestry Administration for Forestry Equipment and Automation, Beijing 100083, China

Funding

National Natural Science Foundation of China · National Natural Science Youth Foundation of China · Special Fund for Beijing Common Construction Project · National Natural

References (42)

Show source-provided references
1. Land use and climate change impacts on global soil erosion by water (2015–2070)10.1073/pnas.2001403117 ↗
2. Lessons from a landmark 1991 article on soil structure: Distinct precedence of non-destructive assessment and benefits of fresh perspectives in soil research10.1071/SR21268 ↗
3. Computed tomography of Archaeopteryx10.1017/S0094837300011921 ↗
4. Variable responses of maize root architecture in elite cultivars due to soil compaction and moisture10.1007/s11104-020-04673-3 ↗
5. A 3D reconstruction method of porous media based on improved WGAN-GP10.1016/j.cageo.2022.105151 ↗
6. An integrated method for 3D reconstruction model of porous geomaterials through 2D CT images10.1016/j.cageo.2018.11.012 ↗
7. A model for soil computed tomography based on volumetric reconstruction, Wiener filtering and parallel processing10.1016/j.compag.2014.12.006 ↗
8. Permeability and microstructure of a saline intact loess after dry-wet cycles10.1155/2021/6653697 ↗
9. The effects of long-term fertilizations on soil hydraulic properties vary with scales10.1016/j.jhydrol.2020.125890 ↗
10. Assessing chromium pollution and natural stabilization processes in agricultural soils by bulk and micro X-ray analyses10.1007/s11356-020-08857-3 ↗
11. X-ray computed tomography imaging of solute movement through ridged and flat plant systems10.1111/ejss.12985 ↗
12. Quantification and characterizing of soil microstructure features by image processing technique10.1016/j.compgeo.2020.103817 ↗
13. Research progress in influencing factors and measuring methods of three-dimensional characteristics of soil macropores
14. Segmentation of digital rock images using deep convolutional autoencoder networks10.1016/j.cageo.2019.02.003 ↗
15. Non-destructive internal disorder segmentation in pear fruit by X-ray radiography and AI10.1016/j.compag.2023.108142 ↗
16. Nondestructive high-throughput sugar beet fruit analysis using X-ray CT and deep learning10.1016/j.compag.2022.107228 ↗
17. A semi-automatic and an automatic segmentation algorithm to remove the internal organs from live pig CT images10.1016/j.compag.2017.06.003 ↗
18. A survey on deep learning in medical image analysis10.1016/j.media.2017.07.005 ↗
19. Deep learning in medical image analysis10.1146/annurev-bioeng-071516-044442 ↗
20. Use of deep learning for structural analysis of computer tomography images of soil samples10.1098/rsos.201275 ↗
21. InDuDoNet+: A deep unfolding dual domain network for metal artifact reduction in CT images10.1016/j.media.2022.102729 ↗
22. Dutta, S., Nwigbo, K.T., Michetti, J., Georgeot, B., Pham, D.H., Kouamé, D., and Basarab, A. (2023, January 4–8). Computed Tomography Image Restoration Using a Quantum-Based Deep Unrolled Denoiser and a Plug-and-Play Framework. Proceedings of the 2023 31st European Signal Processing Conference (EUSIPCO), Helsinki, Finland.10.23919/EUSIPCO58844.2023.10289892 ↗
23. Application of deep learning for semantic segmentation of sandstone thin sections10.1016/j.cageo.2021.104778 ↗
24. Multi-mineral segmentation of micro-tomographic images using a convolutional neural network10.1016/j.cageo.2022.105217 ↗
25. A simplified convolutional network for soil pore identification based on computed tomography imagery10.2136/sssaj2019.04.0119 ↗
26. A novel UNet segmentation method based on deep learning for preferential flow in soil10.1016/j.still.2023.105792 ↗
27. Ronneberger, O., Fischer, P., and Brox, T. (2015, January 5–9). U-net: Convolutional networks for biomedical image segmentation. Proceedings of the Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015: 18th International Conference, Munich, Germany. Proceedings, Part III 18.
28. Zhang, Y., He, Z., Jiang, R., Liao, L., and Meng, Q. (2023). Improved Computer Vision Framework for Mesoscale Simulation of Xiyu Conglomerate Using the Discrete Element Method. Appl. Sci., 13.10.3390/app132413000 ↗
29. Processing of micro-CT images of granodiorite rock samples using convolutional neural networks (CNN), Part II: Semantic segmentation using a 2.5 D CNN10.1016/j.mineng.2023.108027 ↗
30. Automatic segmentation tool for 3D digital rocks by deep learning10.1038/s41598-021-98697-z ↗
31. Çiçek, Ö., Abdulkadir, A., Lienkamp, S.S., Brox, T., and Ronneberger, O. (2016, January 17–21). 3D U-Net: Learning dense volumetric segmentation from sparse annotation. Proceedings of the Medical Image Computing and Computer-Assisted Intervention–MICCAI 2016: 19th International Conference, Athens, Greece. Proceedings, Part II 19.10.1007/978-3-319-46723-8_49 ↗
32. Vu, M.H., Grimbergen, G., Simkó, A., Nyholm, T., and Löfstedt, T. (2019). End-to-End Cascaded U-Nets with a Localization Network for Kidney Tumor Segmentation. arXiv.10.24926/548719.073 ↗
33. Milletari, F., Navab, N., and Ahmadi, S.-A. (2016, January 25–28). V-net: Fully convolutional neural networks for volumetric medical image segmentation. Proceedings of the 2016 Fourth International Conference on 3D Vision (3DV), Stanford, CA, USA.10.1109/3DV.2016.79 ↗
34. Kitrungrotsakul, T., Iwamoto, Y., Han, X.-H., Takemoto, S., Yokota, H., Ipponjima, S., Nemoto, T., Wei, X., and Chen, Y.-W. (2019, January 12–17). A cascade of CNN and LSTM network with 3D anchors for mitotic cell detection in 4D microscopic image. Proceedings of the ICASSP 2019—2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Brighton, UK.10.1109/ICASSP.2019.8682326 ↗
35. Deep sequential segmentation of organs in volumetric medical scans10.1109/TMI.2018.2881678 ↗
36. Stollenga, M.F., Byeon, W., Liwicki, M., and Schmidhuber, J. (2015, January 7–12). Parallel multi-dimensional LSTM, with application to fast biomedical volumetric image segmentation. Proceedings of the 28th International Conference on Neural Information Processing Systems, Montreal, QC, Canada.
37. Chen, J., Yang, L., Zhang, Y., Alber, M., and Chen, D.Z. (2016, January 5–12). Combining fully convolutional and recurrent neural networks for 3d biomedical image segmentation. Proceedings of the 30th International Conference on Neural Information Processing Systems, Barcelona, Spain.
38. Removing segmentation inconsistencies with semi-supervised non-adjacency constraint10.1016/j.media.2019.101551 ↗
39. Effects of freeze-thaw cycles on black soil structure at different size scales
40. Soil pore identification with the adaptive fuzzy C-means method based on computed tomography images10.1007/s11676-018-0725-3 ↗
41. Shi, X., Chen, Z., Wang, H., Yeung, D.-Y., Wong, W.-K., and Woo, W.-C. (2015, January 7–12). Convolutional LSTM network: A machine learning approach for precipitation nowcasting. Proceedings of the 28th International Conference on Neural Information Processing Systems, Montreal, QC, Canada.
42. Lung segmentation in chest radiographs using anatomical atlases with nonrigid registration10.1109/TMI.2013.2290491 ↗