# Towards scalable organ level 3D plant segmentation: Bridging the data algorithm computing gap

arXiv: https://arxiv.org/abs/2509.06329 · HTML: https://mlsanity.com/paper/2509.06329/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 47 of its 184 references that are in the map.
- First posted on arXiv 8 Sep 2025.

## Builds on (most cited first, 30 of 47)

- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [PointNet: Deep Learning on Point Sets for 3D Classification and Segmentation](https://mlsanity.com/paper/1612.00593/) (2016)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [PointNet++: Deep Hierarchical Feature Learning on Point Sets in a Metric Space](https://mlsanity.com/paper/1706.02413/) (2017)
- [ScanNet: Richly-annotated 3D Reconstructions of Indoor Scenes](https://mlsanity.com/paper/1702.04405/) (2017)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [Domain Randomization for Transferring Deep Neural Networks from Simulation to the Real World](https://mlsanity.com/paper/1703.06907/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [4D Spatio-Temporal ConvNets: Minkowski Convolutional Neural Networks](https://mlsanity.com/paper/1904.08755/) (2019)
- [KPConv: Flexible and Deformable Convolution for Point Clouds](https://mlsanity.com/paper/1904.08889/) (2019)
- [PointConv: Deep Convolutional Networks on 3D Point Clouds](https://mlsanity.com/paper/1811.07246/) (2018)
- [Deep Visual Domain Adaptation: A Survey](https://mlsanity.com/paper/1802.03601/) (2018)
- [RandLA-Net: Efficient Semantic Segmentation of Large-Scale Point Clouds](https://mlsanity.com/paper/1911.11236/) (2019)
- [KITTI-360: A Novel Dataset and Benchmarks for Urban Scene Understanding in 2D and 3D](https://mlsanity.com/paper/2109.13410/) (2021)
- [Deep Learning for 3D Point Clouds: A Survey](https://mlsanity.com/paper/1912.12033/) (2019)
- [PartNet: A Large-scale Benchmark for Fine-grained and Hierarchical Part-level 3D Object Understanding](https://mlsanity.com/paper/1812.02713/) (2018)
- [Searching Efficient 3D Architectures with Sparse Point-Voxel Convolution](https://mlsanity.com/paper/2007.16100/) (2020)
- [Point-Voxel CNN for Efficient 3D Deep Learning](https://mlsanity.com/paper/1907.03739/) (2019)
- [PointGroup: Dual-Set Point Grouping for 3D Instance Segmentation](https://mlsanity.com/paper/2004.01658/) (2020)
- [SOLO: Segmenting Objects by Locations](https://mlsanity.com/paper/1912.04488/) (2019)
- [PAConv: Position Adaptive Convolution with Dynamic Kernel Assembling on Point Clouds](https://mlsanity.com/paper/2103.14635/) (2021)
- [SEGCloud: Semantic Segmentation of 3D Point Clouds](https://mlsanity.com/paper/1710.07563/) (2017)
- [OccuSeg: Occupancy-aware 3D Instance Segmentation](https://mlsanity.com/paper/2003.06537/) (2020)
- [Sim-to-Real via Sim-to-Sim: Data-efficient Robotic Grasping via Randomized-to-Canonical Adaptation Networks](https://mlsanity.com/paper/1812.07252/) (2018)
- [SGPN: Similarity Group Proposal Network for 3D Point Cloud Instance Segmentation](https://mlsanity.com/paper/1711.08588/) (2017)
- [Semantic3D.net: A new Large-scale Point Cloud Classification Benchmark](https://mlsanity.com/paper/1704.03847/) (2017)
- [Learning Object Bounding Boxes for 3D Instance Segmentation on Point Clouds](https://mlsanity.com/paper/1906.01140/) (2019)
- [GSPN: Generative Shape Proposal Network for 3D Instance Segmentation in Point Cloud](https://mlsanity.com/paper/1812.03320/) (2018)
- [3D-MPA: Multi Proposal Aggregation for 3D Semantic Instance Segmentation](https://mlsanity.com/paper/2003.13867/) (2020)
- [Hierarchical Aggregation for 3D Instance Segmentation](https://mlsanity.com/paper/2108.02350/) (2021)

## Built on by (most cited first, 1 of 1)

- [PlantC2USeg: Cross-Scale Consistent Pre-Training for Few-Shot Unified Plant Point Cloud Segmentation](https://mlsanity.com/paper/2609.02860/) (2026)

## Abstract (arXiv)

The precise characterization of plant morphology provides valuable insights into plant environment interactions and genetic evolution. A key technology for extracting this information is 3D segmentation, which delineates individual plant organs from complex point clouds. Despite significant progress in general 3D computer vision domains, the adoption of 3D segmentation for plant phenotyping remains limited by three major challenges: i) the scarcity of large-scale annotated datasets, ii) technical difficulties in adapting advanced deep neural networks to plant point clouds, and iii) the lack of standardized benchmarks and evaluation protocols tailored to plant science. This review systematically addresses these barriers by: i) providing an overview of existing 3D plant datasets in the context of general 3D segmentation domains, ii) systematically summarizing deep learning-based methods for point cloud semantic and instance segmentation, iii) introducing Plant Segmentation Studio (PSS), an open-source framework for reproducible benchmarking, and iv) conducting extensive quantitative experiments to evaluate representative networks and sim-to-real learning strategies. Our findings highlight the efficacy of sparse convolutional backbones and transformer-based instance segmentation, while also emphasizing the complementary role of modeling-based and augmentation-based synthetic data generation for sim-to-real learning in reducing annotation demands. In general, this study bridges the gap between algorithmic advances and practical deployment, providing immediate tools for researchers and a roadmap for developing data-efficient and generalizable deep learning solutions in 3D plant phenotyping. Data and code are available at https://github.com/perrydoremi/PlantSegStudio.