A novel mesh processing based technique for 3D plant analysis

BMC Plant Biology

Volumn 12, Issue , 2012, Pages

  Paproki, Anthony ^a   Sirault, Xavier ^a   Berry, Scott ^a   Furbank, Robert ^a   Fripp, Jurgen ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DICOTYLEDONEAE; GOSSYPIUM HIRSUTUM;

ALGORITHM; ARTICLE; COMPARATIVE STUDY; GOSSYPIUM; GROWTH, DEVELOPMENT AND AGING; HISTOLOGY; IMAGE PROCESSING; INFORMATION PROCESSING; METHODOLOGY; PHENOTYPE; PLANT LEAF; PLANT STEM; THREE DIMENSIONAL IMAGING; TIME;

ALGORITHMS; AUTOMATIC DATA PROCESSING; GOSSYPIUM; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; PHENOTYPE; PLANT LEAVES; PLANT STEMS; TIME FACTORS;

EID: 84860363173     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-12-63     Document Type: Article

References (41)

1. Furbank RT, Tester M. Phenomics - technologies to relieve the phenotyping bottleneck. Trends Plant Sci 2011, 16(12):635. 10.1016/j.tplants.2011.09.005, 22074787.
2. Granier C, Tardieu F. Multi-scale phenotyping of leaf expansion in response to environmental changes: the whole is more than the sum of parts. Plant Cell Environ 2009, 32(9):1175. 10.1111/j.1365-3040.2009.01955.x, 19210637.
3. Schurr U, Heckenberger U, Herdel K, Walter A, Feil R. Leaf development in Ricinus communis during drought stress: dynamics of growth processes, of cellular structure and of sink-source transition. J Exp Bot 2000, 51(350):1515. 10.1093/jexbot/51.350.1515, 11006303.
4. Vos J, Evers JB, Buck-Sorlin GH, Andrieu B, Chelle M, de Visser PHB. Functional-structural plant modelling: a new versatile tool in crop science. J Exp Bot 2010, 61(8):2101. 10.1093/jxb/erp345, 19995824.
5. Eberius M, Lima-Guerra J. High-Throughput plant phenotyping-data acquisition, transformation, and analysis. Bioinformatics 2009, 259.
6. Duan L, Yang W, Huang C, Liu Q. A novel machine-vision-based facility for the automatic evaluation of yield-related traits in rice. Plant Methods 2011, 7:44. 10.1186/1746-4811-7-44, 3264518, 22152096.
7. Granier C, Aguirrezabal L, Chenu K, Cookson S, Dauzat M, Hamard P, Thioux J, Rolland G, Bouchier-Combaud S, Lebaudy A, et al. PHENOPSIS, an automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit. New Phytologist 2006, 169(3):623. 10.1111/j.1469-8137.2005.01609.x, 16411964.
8. Walter A, Scharr H, Gilmer F, Zierer R, Nagel K, Ernst M, Wiese A, Virnich O, Christ M, Uhlig B, et al. Dynamics of seedling growth acclimation towards altered light conditions can be quantified via GROWSCREEN: a setup and procedure designed for rapid optical phenotyping of different plant species. New Phytologist 2007, 174(2):447. 10.1111/j.1469-8137.2007.02002.x, 17388907.
9. Jansen M, Gilmer F, Biskup B, Nagel KA, Rascher U, Fischbach A, Briem S, Dreissen G, Tittmann S, Braun S, De Jaeger I, Metzlaff M, Schurr U, Scharr H, Walter A. Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance in Arabidopsis thaliana and other rosette plants. Funct Plant Biol 2009, 36(11):902.
10. Bylesjö M, Segura V, Soolanayakanahally R, Rae A, Trygg J, Gustafsson P, Jansson S, Street N. LAMINA: a tool for rapid quantification of leaf size and shape parameters. BMC Plant Biol 2008, 8:82. 10.1186/1471-2229-8-82, 2500018, 18647399.
11. Reuzeau C, Pen J, Frankard V, de Wolf J, Peerbolte R, Broekaert W. TraitMill: a discovery engine for identifying yield-enhancement genes in cereals. Fenzi Zhiwu Yuzhong (Mol Plant Breeding) 2005, 3:7534.
12. Hartmann A, Czauderna T, Hoffmann R, Stein N, Schreiber F. HTPheno: An image analysis pipeline for high-throughput plant phenotyping. BMC Bioinf 2011, 12:148.
13. Yang W, Xu X, Duan L, Luo Q, Chen S, Zeng S, Liu Q. High-throughput measurement of rice tillers using a conveyor equipped with x-ray computed tomography. Rev Sci Instrum 2011, 82(2):025102. 10.1063/1.3531980, 21361628.
14. Naeem A, French A, Wells D, Pridmore T. High-throughput feature counting and measurement of roots. Bioinformatics 2011, 27(9):1337. 10.1093/bioinformatics/btr126, 21398671.
15. Yazdanbakhsh N, Fisahn J. High throughput phenotyping of root growth dynamics, lateral root formation, root architecture and root hair development enabled by PlaRoM. Funct Plant Biol 2009, 36(11):938.
16. Iyer-Pascuzzi A, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz J, Benfey P. Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiol 2010, 152(3):1148. 10.1104/pp.109.150748, 2832248, 20107024.
17. Biskup B, Scharr H, Fischbach A, Wiese-Klinkenberg A, Schurr U, Walter A. Diel growth cycle of isolated leaf discs analyzed with a novel, high-throughput three-dimensional imaging method is identical to that of intact leaves. Plant Physiol 2009, 149(3):1452. 10.1104/pp.108.134486, 2649408, 19168641.
18. Clark R, Maccurdy R, Jung J, Shaff J, McCouch S, Aneshansley D, Kochian L. Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 2011, 156(10):455. 3177249, 21454799.
19. Wang H, Zhang W, Zhou G, Yan G, Clinton N. Image-based 3D corn reconstruction for retrieval of geometrical structural parameters. Int J Remote Sensing 2009, 30(20):5505.
20. Huang Q, Stockman GC. Generalized tube model: recognizing 3D elongated objects from 2D intensity images. PROCEEDINGS CVPR IEEE 1993, 104-109. , .
21. Huang Q, Jain A, Stockman G, Smucker A. Automatic image analysis of plant root structures. Pattern Recognition, 1992. Vol.II. Conference B: Pattern Recognition Methodology and Systems, Proceedings., 11th IAPR International Conference on 1992, 569-572. , .
22. Nathalie W, Jean-Christophe P. High-contrast three-dimensional imaging of the Arabidopsis leaf enables the analysis of cell dimensions in the epidermis and mesophyll. Plant Methods 2010, 6(17):1. 2829548, 20180960.
23. Baumberg A, Lyons A, Taylor R. 3D SOM-A commercial software solution to 3D scanning. Graphical Models 2005, 67(6):476.
24. Shamir A. A survey on Mesh Segmentation Techniques. Computer Graphics Forum 2008, 27(6):1539.
25. Golovinskiy A, Funkhouser T. Consistent Segmentation of 3D Models. Comput Graphics (Shape Modeli Int) 2009, 33(3):262.
26. Cornelissen JHC, Lavorel S, Garnier E, Díaz S, Buchmann N, Gurvich DE, Reich PB, Steege HT, Morgan HD, Heijden M, Pausas JG, Poorter H. A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Aust J Bot 2003, 51(4):335.
27. Niem W, Wingbermuhle J. Automatic reconstruction of 3D objects using a mobile monoscopic camera. 3-D Digital Imaging and Modeling, 1997. Proceedings., International Conference on Recent Advances in IEEE 1999, 173-180. , .
28. The PlantScan Webpage , http://www.plantphenomics.org.au/node/157
29. Franco J, Boyer E. Fusion of multiview silhouette cues using a space occupancy grid. Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on, Volume 2 IEEE 2005, 1747-1753. , .
30. Kolev K, Klodt M, Brox T, Cremers D. Continuous global optimization in multiview 3d reconstruction. Int J Comput Vision 2009, 84:80.
31. Hosoi F, Omasa K. Voxel-Based 3-D modeling of individual trees for estimating leaf area density using high-resolution portable scanning lidar. Geoscience Remote Sensing, IEEE Transact on 2006, 44(12):3610.
32. Vieira M, Shimada K. Surface mesh segmentation and smooth surface extraction through region growing. Comput Aided Geometric Des 2005, 22(8):771.
33. Attene M, Falcidieno B, Spagnuolo M. Hierarchical mesh segmentation based on fitting primitives. Visual Comput 2006, 22(3):181.
34. Mortara M, Patané G, Spagnuolo M, Falcidieno B, Rossignac J. Plumber: a method for a multi-scale decomposition of 3D shapes into tubular primitives and bodies. Proceedings of the ninth ACM symposium on Solid modeling and applications 2004, 339-344. , .
35. Kuhn H The Hungarian method for the assignment problem. Naval Res Logistics Q 1955, 2(1-2):83. Kuhn H.
36. Rodgers J, Nicewander W. Thirteen ways to look at the correlation coefficient. Am Statistician 1988, 42(1):59.
37. Koch G Intraclass correlation coefficient. Encyclopedia Stat Sci 1983, 4:212. Koch G.
38. Shrout P, Fleiss J. Intraclass correlations: uses in assessing rater reliability. Psychological Bull 1979, 86(2):420.
39. Bartko J The intraclass correlation coefficient as a measure of reliability. Psychological R 1966, 19:3. Bartko J.
40. Danjon F, Reubens B. Assessing and analyzing 3D architecture of woody root systems, a review of methods and applications in tree and soil stability, resource acquisition and allocation. Plant Soil 2008, 303:1.
41. Pradal C, Dufour-Kowalski S, Boudon F, Fournier C, Godin C. OpenAlea: a visual programming and component-based software platform for plant modelling. Funct Plant Biol 2008, 35(10):751.