Simplification of leaf surfaces from scanned data: Effects of two algorithms on leaf morphology

Computers and Electronics in Agriculture

Volumn 121, Issue , 2016, Pages 393-403

  Hou, Tongyu ^a   Zheng, Bangyou ^b   Xu, Zhaoli ^c   Yang, Yuhong ^c   Chen, Yan ^a   Guo, Yan ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b CSIRO   (Australia)

^c Yunnan Academy of Tobacco Agricultural Sciences   (China)

Author keywords

Functional structural plant modelling; Leaf geometry; Leaf surface model; Light interception; Mesh simplification; Plant phenotyping

Indexed keywords

ALGORITHMS; DIGITAL STORAGE; ERRORS; LASER APPLICATIONS; MORPHOLOGY; STEREO IMAGE PROCESSING; SURFACE ANALYSIS; SURFACE MORPHOLOGY;

FUNCTIONAL STRUCTURAL PLANT MODELLING; LEAF SURFACES; LIGHT INTERCEPTION; MESH SIMPLIFICATIONS; PLANT PHENOTYPING;

PLANTS (BOTANY);

ALGORITHM; DATA SET; GEOMETRY; LASER METHOD; LEAF MORPHOLOGY; MAIZE; OPTIMIZATION; PHENOTYPE; SCANNER; STEREO IMAGE; THREE-DIMENSIONAL MODELING; TOBACCO;

NICOTIANA TABACUM; ZEA MAYS;

EID: 84954568945     PISSN: 01681699     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compag.2016.01.010     Document Type: Article

References (59)

1. Araus J.L., Cairns J.E. Field high-throughput phenotyping: the new crop breeding frontier. Trends Plant Sci. 2014, 19:52-61. 10.1016/j.tplants.2013.09.008.
2. Armon S., Yanai O., Ori N., Sharon E. Quantitative phenotyping of leaf margins in three dimensions, demonstrated on KNOTTED and TCP trangenics in Arabidopsis. J. Exp. Bot. 2014, 65:2071-2077. 10.1093/jxb/eru062.
3. Bellasio C., Olejníčková J., Tesař R., Šebela D., Nedbal L. Computer reconstruction of plant growth and chlorophyll fluorescence emission in three spatial dimensions. Sensors-Basel 2012, 12:1052-1071. 10.3390/s120101052.
4. Bennetzen J.L., Chandler V.L., Schnable P. National science foundation-sponsored workshop report. Maize genome sequencing project. Plant Physiol. 2001, 127:1572-1578. 10.1104/pp.010817.
5. 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, 149:1452-1461. 10.1104/pp.108.134486.
6. Biskup B., Scharr H., Schurr U., Rascher U.W.E. A stereo imaging system for measuring structural parameters of plant canopies. Plant, Cell Environ. 2007, 30:1299-1308.
7. Bussière F., Solmon F., Fouéré A. Implementation and evaluation of DROP, a model for the simulation of rainfall distribution below plants described in 3D. Agronomie 2002, 22:93-103. 10.1051/agro:2001002.
8. Chambelland J., Dassot M., Adam B., Donès N., Balandier P., Marquier A., Saudreau M., Sonohat G., Sinoquet H. A double-digitising method for building 3D virtual trees with non-planar leaves: application to the morphology and light-capture properties of young beech trees (Fagus sylvatica). Funct. Plant Biol. 2008, 35:1059-1069.
9. Chelle M. Phylloclimate or the climate perceived by individual plant organs: What is it? How to model it? What for?. New Phytol. 2005, 166:781-790. 10.1111/j.1469-8137.2005.01350.x.
10. Cignoni P., Rocchini C., Scopigno R. Metro: measuring error on simplified surfaces. Comput. Graph. Forum 1998, 17:167-174. 10.1111/1467-8659.00236.
11. Darula S., Kittler R. CIE general sky standard defining luminance distributions. Proc. eSim 2002, 11-13.
12. Dauzat J., Rapidel B., Berger A. Simulation of leaf transpiration and sap flow in virtual plants: model description and application to a coffee plantation in Costa Rica. Agric. Forest Meteorol. 2001, 109:143-160. 10.1016/S0168-1923(01)00236-2.
13. Dhondt S., Wuyts N., Inzé D. Cell to whole-plant phenotyping: the best is yet to come. Trends Plant Sci. 2013, 18:428-439. 10.1016/j.tplants.2013.04.008.
14. Digne J., Cohen-Steiner D., Alliez P., de Goes F., Desbrun M. Feature-preserving surface reconstruction and simplification from defect-laden point sets. J. Math. Imag. Vis. 2014, 48:369-382. 10.1007/s10851-013-0414-y.
15. Dorr, G.J., Kempthorne, D.M., Mayo, L.C., Forster, W.A., Zabkiewicz, J.A., McCue, S.W., Belward, J.A., Turner, I.W., Hanan, J., 2014. Towards a model of spray-canopy interactions: Interception, shatter, bounce and retention of droplets on horizontal leaves. In: Ecol Model, Special Issue of the 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA'12) Special Issue of PMA'12 290, pp. 94-101. doi:10.1016/j.ecolmodel.2013.11.002.
16. Eitel J.U.H., Vierling L.A., Long D.S. Simultaneous measurements of plant structure and chlorophyll content in broadleaf saplings with a terrestrial laser scanner. Remote Sens. Environ. 2010, 114:2229-2237. 10.1016/j.rse.2010.04.025.
17. Erikson, C., 1996. Polygonal Simplification: An Overview (Technical Report No. TR96-106). University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
18. España M., Baret F., Aries F., Andrieu B., Chelle M. Radiative transfer sensitivity to the accuracy of canopy structure description. The case of a maize canopy. Agronomie 1999, 19:241-254. 10.1051/agro:19990305.
19. Falster D.S., Westoby M. Leaf size and angle vary widely across species: what consequences for light interception?. New Phytol. 2003, 158:509-525.
20. Fiorani F., Rascher U., Jahnke S., Schurr U. Imaging plants dynamics in heterogenic environments. Curr. Opin. Biotechnol. 2012, 23:227-235. Food biotechnology - Plant biotechnology. 10.1016/j.copbio.2011.12.010.
21. Fiorani F., Schurr U. Future scenarios for plant phenotyping. Annu. Rev. Plant Biol. 2013, 64:267-291. 10.1146/annurev-arplant-050312-120137.
22. Ford E.D., Cocke A., Horton L., Fellner M., Van Volkenburgh E. Estimation, variation and importance of leaf curvature in Zea mays hybrids. Agric. Forest Meteorol. 2008, 148:1598-1610. 10.1016/j.agrformet.2008.05.015.
23. Fournier C., Pradal C. A plastic, dynamic and reducible 3D geometric model for simulating gramineous leaves. International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications 2012, 125-132. IEEE, Shangai, China. K. Mengzheng (Ed.).
24. Furbank R.T., Tester M. Phenomics - technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 2011, 16:635-644. 10.1016/j.tplants.2011.09.005.
25. Garland M., Heckbert P.S. Surface simplification using quadric error metrics. Proceedings of the 24th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH '97 1997, 209-216. ACM Press/Addison-Wesley Publishing Co., New York, NY, USA. 10.1145/258734.258849.
26. Hanan J.S., Loch B., McAleer T. Processing laser scanner plant data to extract structural information. Proceedings of the 4th International Workshop on Functional Structural Plant Models (FSPM04). Presented at the 4th International Workshop on Functional Structural Plant Models (FSPM04) 2004, 9-12. INRA/CIRAD AMAP, Montpellier, France. C. Godin, J.S. Hanan, W. Kurth (Eds.).
27. Kadioglu A., Terzi R., Saruhan N., Saglam A. Current advances in the investigation of leaf rolling caused by biotic and abiotic stress factors. Plant Sci. 2012, 182:42-48. Abiotic stress tolerances. 10.1016/j.plantsci.2011.01.013.
28. Kempthorne D.M., Barry M., Zabkiewicz J.A., Young J. 3D digitisation of plant leaves. ANZIAM J 2014, 55:138-152. 10.0000/anziamj.v55i0.7850.
29. Lewis P. 3D canopy modelling as a tool in remote-sensing research. Functional-Structural Plant Modelling in Crop Production. Presented at the 7th International Workshop on Functional Structural Plant Models (FSPM07) 2007, 219-229. Springer, Netherlands.
30. Liu Z.Y., Jia L.G., Mao Y.F., He Y.K. Classification and quantification of leaf curvature. J. Exp. Bot. 2010, 61:2757-2767. 10.1093/jxb/erq111.
31. Llorens J., Gil E., Llop J., Escolà A. Ultrasonic and LIDAR sensors for electronic canopy characterization in vineyards: advances to improve pesticide application methods. Sensors-Basel 2011, 11:2177-2194. 10.3390/s110202177.
32. Loch, B.I., Belward, J.A., Hanan, J.S., 2005. Application of Surface Fitting Techniques for the Representation of Leaf Surfaces. In: Presented at the MODSIM05, Modelling and Simulation Society of Australia and New Zealand, pp. 1272-1278.
33. Luebke D.P. A developer's survey of polygonal simplification algorithms. IEEE Comput Graph 2001, 21:24-35. 10.1109/38.920624.
34. Massinon M., Dumont B., De Cock N., Salah S.O.T., Lebeau F. Study of retention variability on an early growth stage herbaceous plant using a 3D virtual spraying model. Crop Prot. 2015, 78:63-71. 10.1016/j.cropro.2015.08.018.
35. Nilson T. A theoretical analysis of the frequency of gaps in plant stands. Agric. Forest Meteorol. 1971, 8:25-38. 10.1016/0002-1571(71)90092-6.
36. Omasa K., Hosoi F., Konishi A. 3D lidar imaging for detecting and understanding plant responses and canopy structure. J. Exp. Bot. 2007, 58:881-898. 10.1093/jxb/erl142.
37. Oqielat M.N., Turner I.W., Belward J.A. A hybrid Clough-Tocher method for surface fitting with application to leaf data. Appl. Math. Model. 2009, 33:2582-2595. 10.1016/j.apm.2008.07.023.
38. Oqielat M.N., Turner I.W., Belward J.A., McCue S.W. Modelling water droplet movement on a leaf surface. Math. Comput. Simulat. 2011, 81:1553-1571. 10.1016/j.matcom.2010.09.003.
39. Paproki A., Sirault X., Berry S., Furbank R., Fripp J. A novel mesh processing based technique for 3D plant analysis. BMC Plant Biol. 2012, 12:63. 10.1186/1471-2229-12-63.
40. Paulus S., Schumann H., Kuhlmann H., Léon J. High-precision laser scanning system for capturing 3D plant architecture and analysing growth of cereal plants. Biosyst. Eng. 2014, 121:1-11. 10.1016/j.biosystemseng.2014.01.010.
41. Pearcy R.W., Muraoka H., Valladares F. Crown architecture in sun and shade environments: assessing function and trade-offs with a three-dimensional simulation model. New Phytol. 2005, 166:791-800.
42. Rossignac J., Borrel P. Multi-resolution 3D approximations for rendering complex scenes. Modeling in Computer Graphics, IFIP Series on Computer Graphics 1993, 455-465. Springer, Berlin, Heidelberg. D.B. Falcidieno, P.D.T.L. Kunii (Eds.).
43. Sarlikioti V., de Visser P., Buck-Sorlin G., Marcelis L. How plant architecture affects light absorption and photosynthesis in tomato: towards an ideotype for plant architecture using a functional-structural plant model. Ann. Bot.-London 2011, 108:1065-1073.
44. Schaeffer S., Koepke T., Dhingra A. Tobacco: a model plant for understanding the mechanism of abiotic stress tolerance. Improving Crop Resistance to Abiotic Stress 2012, 1169-1201. Wiley-VCH Verlag GmbH & Co. KGaA. N. Tuteja, S.S. Gill, A.F. Tiburcio, R. Tuteja (Eds.).
45. Schöler F., Steinhage V. Automated 3D reconstruction of grape cluster architecture from sensor data for efficient phenotyping. Comput. Electron. Agric. 2015, 114:163-177.
46. Schroeder W.J., Avila L.S., Hoffman W. Visualizing with VTK: a tutorial. IEEE Comput. Graph. 2000, 20:20-27. 10.1109/38.865875.
47. Schroeder W.J., Zarge J.A., Lorensen W.E. Decimation of triangle meshes. Proceedings of the 19th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH '92 1992, 65-70. ACM, New York, NY, USA. 10.1145/133994.134010.
48. Silva D.D., Han L.Q., Faivre R., Costes E. Influence of the variation of geometrical and topological traits on light interception efficiency of apple trees: sensitivity analysis and metamodelling for ideotype definition. Ann. Bot. 2014, 114:739-752. 10.1093/aob/mcu034.
49. Strable J., Scanlon M.J. Maize (Zea mays): a model organism for basic and applied research in plant biology. Cold Spring Harb. Protoc. 2009, 2009:33-41. 10.1101/pdb.emo132.
50. Van Elewijck L. Influence of leaf and branch slope on Stemflow amount. CATENA 1989, 16:525-533. Selected papers of the Fourth Benelux Colloquium on Geomorphological Processes. 10.1016/0341-8162(89)90033-7.
51. Wang H.X., Zhang W.M., Zhou G.Q., Yan G.J., Clinton N. Image-based 3D corn reconstruction for retrieval of geometrical structural parameters. Int. J. Remote Sens. 2009, 30:5505-5513. 10.1080/01431160903130952.
52. Wang X.P., Guo Y., Li B.G., Wang X.Y., Ma Y.T. Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies. Int. J. Biometeorol. 2006, 50:349-357.
53. Wang Y.P. A comparison of three different canopy radiation models commonly used in plant modelling. Funct. Plant Biol. 2003, 30:143-152.
54. Wei J., Lou Y. Feature preserving mesh simplification using feature sensitive metric. J. Comput. Sci. Technol. 2010, 25:595-605. 10.1007/s11390-010-9348-7.
55. Zhang J., Li G.H., Song Y.P., Liu Z.H., Yang C.D., Tang S., Zheng C.Y., Wang S.H., Ding Y.F. Lodging resistance characteristics of high-yielding rice populations. Field Crops Res. 2014, 161:64-74. 10.1016/j.fcr.2014.01.012.
56. Zheng B.Y., Ma Y.T., Li B.G., Guo Y., Deng Q.Y. Assessment of the influence of global dimming on the photosynthetic production of rice based on three-dimensional modeling. Sci. China Earth Sci. 2011, 54:290-297. 10.1007/s11430-010-4097-6.
57. Zheng B.Y., Shi L.J., Ma Y.T., Deng Q.Y., Li B.G., Guo Y. Comparison of architecture among different cultivars of hybrid rice using a spatial light model based on 3-D digitising. Funct. Plant Biol. 2008, 35:900-910.
58. Zhou, L.X., Pang, A., 2001. Metrics and visualization tools for surface mesh comparison. In: Proc. SPIE 4302. Presented at the Visual Data Exploration and Analysis, Visual Data Exploration and Analysis VIII, pp. 99-110. doi:10.1117/12.424920.
59. Zou X.C., Mõttus M., Tammeorg P., Torres C.L., Takala T., Pisek J., Mäkelä P., Stoddard F.L., Pellikka P. Photographic measurement of leaf angles in field crops. Agric. Forest Meteorol. 2014, 184:137-146. 10.1016/j.agrformet.2013.09.010.