Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds
Modern plant phenotyping requires tools that are robust to noise and missing data, while being able to efficiently process large numbers of plants. Here, we studied the skeletonization of plant architectures from 3D point clouds, which is critical for many downstream tasks, including analyses of pla...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | Remote Sensing |
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| Online Access: | https://www.mdpi.com/2072-4292/13/19/3802 |
| _version_ | 1797515875602923520 |
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| author | Illia Ziamtsov Kian Faizi Saket Navlakha |
| author_facet | Illia Ziamtsov Kian Faizi Saket Navlakha |
| author_sort | Illia Ziamtsov |
| collection | DOAJ |
| description | Modern plant phenotyping requires tools that are robust to noise and missing data, while being able to efficiently process large numbers of plants. Here, we studied the skeletonization of plant architectures from 3D point clouds, which is critical for many downstream tasks, including analyses of plant shape, morphology, and branching angles. Specifically, we developed an algorithm to improve skeletonization at branch points (forks) by leveraging the geometric properties of cylinders around branch points. We tested this algorithm on a diverse set of high-resolution 3D point clouds of tomato and tobacco plants, grown in five environments and across multiple developmental timepoints. Compared to existing methods for 3D skeletonization, our method efficiently and more accurately estimated branching angles even in areas with noisy, missing, or non-uniformly sampled data. Our method is also applicable to inorganic datasets, such as scans of industrial pipes or urban scenes containing networks of complex cylindrical shapes. |
| first_indexed | 2024-03-10T06:53:25Z |
| format | Article |
| id | doaj.art-c7f8acbd0990460aae6c4f36a94c760a |
| institution | Directory Open Access Journal |
| issn | 2072-4292 |
| language | English |
| last_indexed | 2024-03-10T06:53:25Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Remote Sensing |
| spelling | doaj.art-c7f8acbd0990460aae6c4f36a94c760a2023-11-22T16:41:04ZengMDPI AGRemote Sensing2072-42922021-09-011319380210.3390/rs13193802Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point CloudsIllia Ziamtsov0Kian Faizi1Saket Navlakha2Integrative Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USAIntegrative Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USACold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY 11724, USAModern plant phenotyping requires tools that are robust to noise and missing data, while being able to efficiently process large numbers of plants. Here, we studied the skeletonization of plant architectures from 3D point clouds, which is critical for many downstream tasks, including analyses of plant shape, morphology, and branching angles. Specifically, we developed an algorithm to improve skeletonization at branch points (forks) by leveraging the geometric properties of cylinders around branch points. We tested this algorithm on a diverse set of high-resolution 3D point clouds of tomato and tobacco plants, grown in five environments and across multiple developmental timepoints. Compared to existing methods for 3D skeletonization, our method efficiently and more accurately estimated branching angles even in areas with noisy, missing, or non-uniformly sampled data. Our method is also applicable to inorganic datasets, such as scans of industrial pipes or urban scenes containing networks of complex cylindrical shapes.https://www.mdpi.com/2072-4292/13/19/3802skeleton graph extractionplant phenotyping3D point clouds3D shape decompositionLiDAR |
| spellingShingle | Illia Ziamtsov Kian Faizi Saket Navlakha Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds Remote Sensing skeleton graph extraction plant phenotyping 3D point clouds 3D shape decomposition LiDAR |
| title | Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds |
| title_full | Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds |
| title_fullStr | Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds |
| title_full_unstemmed | Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds |
| title_short | Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds |
| title_sort | branch pipe improving graph skeletonization around branch points in 3d point clouds |
| topic | skeleton graph extraction plant phenotyping 3D point clouds 3D shape decomposition LiDAR |
| url | https://www.mdpi.com/2072-4292/13/19/3802 |
| work_keys_str_mv | AT illiaziamtsov branchpipeimprovinggraphskeletonizationaroundbranchpointsin3dpointclouds AT kianfaizi branchpipeimprovinggraphskeletonizationaroundbranchpointsin3dpointclouds AT saketnavlakha branchpipeimprovinggraphskeletonizationaroundbranchpointsin3dpointclouds |