Analyzing Growing Plants from 4D Point Cloud Data

ACM ToG 2013(Proc. of SIGGRAPH Asia 2013)

Yangyan Li*          Xiaochen Fan*                 Niloy J. Mitra                  Daniel Chamovitz                 Daniel Cohen-Or                 Baoquan Chen*,†
*Shenzhen VisuCA Key Lab/SIAT      University College London      Plant Biosciences, TAU      Computer Science, TAU      Shandong University

Figure 1: Dishlia growth time lapse point cloud over 5 weeks, with classified organs and detected budding, bifurcation and decay events (top row). The extracted growth events are used to synthesize a live plant model from a static model, brought to life with both motion and growth (bottom row).

Abstract

Studying growth and development of plants is of central importance in botany. Current methods for quantitative analysis of such growth processes are either limited to tedious and sparse manual measurements, or coarse image-based 2D measurements. Availability of cheap and portable 3D acquisition devices has the potential to automate this process and easily provide scientists with volumes of accurate data, at a scale much beyond the realms of existing methods. However, during their development, plants grow new parts (e.g., vegetative buds) and bifurcate to different components—violating the central incompressibility assumption made by existing acquisition algorithms, which makes these algorithms unsuited for analyzing growth. We introduce a framework to study plant growth, particularly focusing on accurate localization and tracking topological events like budding and bifurcation. This is achieved by a novel forward-backward analysis, wherein we track robustly detected plant components back in time to ensure correct spatio-temporal event detection using a locally adapting threshold. We evaluate our approach on several groups of time lapse scans, often ranging from days to weeks, on a diverse set of plant species and use the results to animate static virtual plants or directly attach them to physical simulators.

Video

Video source from: Or

Paper and Slides

Paper: 30M PDF
Slides: 224M PDF

Data

To the best of our knowledge, this is the first 4D data of growing plants. Coming soon...

Acknowledgements

We are grateful to Zhan Song, Xufang Pang and Xiaoting Zhang for helping build the structured light scanning system, Jernej Barbič and Yili Zhao for running their plant simulator on our data, Sujuan Tan(her flower shop) for taking care of the plants, Amit Shesh and Nathan Gossett for proofreading the paper. We would like to thank all the reviewers for their valuable comments.

This work is supported in part by grants from NSFC(61202221, 61232011, 61161160567), National 863 Program(2013AA01A604), Guangdong Science and Technology Program(2011B050200007), Shenzhen Innovation Program(CXB201104220029A, ZD201111080115A, KC2012JSJS0019A, KQCX20120807104901791, JCYJ20120617114842361), Israeli science foundation, Marie Curie CIG and ERC Starting Grant SmartGeometry.

BibTex

@ARTICLE{Planalyze2013,
  title = {Analyzing Growing Plants from 4D Point Cloud Data},
  author = {Yangyan Li and Xiaochen Fan and Niloy J. Mitra and Daniel Chamovitz and Daniel Cohen-Or and Baoquan Chen},
  journal = {ACM Transactions on Graphics (Proceedings of SIGGRAPH Asia 2013)},
  volume = {32},
  issue = {6},
  pages = {},
  year = {2013},
  url={http://doi.acm.org/10.1145/2508363.2508368},
  doi={10.1145/2508363.2508368}
}