Comparison of threshold algorithms for automatic image processing of rice roots using freeware ImageJ

Field Crops Research

Volumn 121, Issue 3, 2011, Pages 460-463

  Tajima, Ryosuke ^a   Kato, Yoichiro ^b  

^a TOHOKU UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Image analysis; ImageJ; Root length; Thresholding algorithm; WinRHIZO

Indexed keywords

ALGORITHM; COMPARATIVE STUDY; DIGITAL IMAGE; FUNCTIONAL MORPHOLOGY; IMAGE PROCESSING; PHENOTYPE; RICE; ROOT SYSTEM; SOFTWARE; THRESHOLD; UPLAND REGION;

EID: 79952708985     PISSN: 03784290     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fcr.2011.01.015     Document Type: Article

References (32)

1. Adachi S., Tsuru Y., Kondo M., Yamamoto T., Arai-Sanoh Y., Ando T., Ookawa T., Yano M., Hirasawa T. Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines. Ann. Bot. 2010, 106:803-811.
2. Bouma T.J., Nielsen K.L., Koutstaal B. Sample preparation and scanning protocol for computerized analysis of root length and diameter. Plant Soil 2000, 218:185-196.
3. Doyle W. Operation useful for similarity-invariant pattern recognition. J. Assoc. Comput. Mach. 1962, 9:259-267.
4. Gewin V. An underground revolution. Nature 2010, 466:552-553.
5. Glasbey C.A. An analysis of histogram-based thresholding algorithms. Graph. Models Image Process. 1993, 55:532-537.
6. Hayashi S., Kamoshita A., Yamagishi J., Kotchasatit A., Jongdee B. Genotypic differences in grain yield of transplanted and direct-seeded rainfed lowland rice (Oryza sativa L.) in northeastern Thailand. Field Crops Res. 2007, 102:9-21.
7. Henry A., Gowda V.R.P., Torres R.O., McNally K.L., Serraj R. Variation in root system architecture and drought response in rice (Oryza sativa): phenotyping of the OryzaSNP panel in rainfed lowland fields. Field Crops Res. 2011, 120:205-214.
8. Horii H., Nemoto K., Miyamoto N., Harada J. Quantitative trait loci for adventitious and lateral roots in rice. Plant Breed. 2006, 125:198-200.
9. Huang L.-K., Wang M.-J.J. Image thresholding by maximizing the index of nonfuzziness of the 2-D grayscale histogram. Pattern Recognit. 1995, 28:41-51.
10. Izumi Y., Yoshida T., Iijima M. Effects of subsoiling to the non-tilled field of wheat-soybean rotation on the root system development, water uptake, and yield. Plant Prod. Sci. 2009, 12:327-335.
11. Kano, M., Inukai, Y., Kitano, H., Yamauchi, A., 2011 Root plasticity as the key root trait for adaptation to various intensities of drought stress in rice. Plant Soil, in press, http://www.springerlink.com/content/w45855x53107500u/.
12. Kapur J.N., Sahoo P.K., Wong A.C.K. A new method for gray-level picture thresholding using the entropy of the histogram. Graph. Models Image Process. 1985, 29:273-285.
13. Kato Y., Okami M., Tajima R., Fujita D., Kobayashi N. Root response to aerobic conditions in rice, estimated by Comair root length scanner and scanner-based image analysis. Field Crops Res. 2010, 118:194-198.
14. Kaspar T.C., Ewing R.P. ROOTEDGE: software for measuring root length from desktop scanner images. Agron. J. 1997, 89:932-940.
15. Kimura K., Kikuchi S., Yamasaki S. Accurate root length measurement by image analysis. Plant Soil 1999, 216:117-127.
16. Kittler J., Illingworth J. Minimum error thresholding. Pattern Recognit. 1986, 19:41-47.
17. Le Bot J., Serra V., Fabre J., Draye X., Adamowicz S., Pagès L. DART: a software to analyze root system architecture and development from captured images. Plant Soil 2010, 326:261-273.
18. Li C.H., Tam P.K.S. An iterative algorithm for minimum cross entropy thresholding. Pattern Recognit. Lett. 1998, 18:771-776.
19. Lynch J.P. Roots of the second green revolution. Aust. J. Bot. 2007, 55:493-512.
20. Otsu N. A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 1979, 9:62-66.
21. Pan W.L., Bolton R.P. Root quantification by edge discrimination using a desktop scanner. Agron. J. 1991, 83:1047-1052.
22. Padilla F.M., Miranda J.D., Jorquera M.J., Pugnaire F.I. Variability in amount and frequency of water supply affects roots but not growth of arid shrubs. Plant Ecol. 2009, 204:261-270.
23. Prewitt J.M.S., Mendelsohn M.L. The analysis of cell images. Ann. N. Y. Acad. Sci. 1966, 128:1035-1053.
24. Ridler T.W., Calvard S. Picture thresholding using an iterative selection method. IEEE Trans. Syst. Man Cybern. 1978, 8:630-632.
25. Sekiya N., Yano K. Seed P-enrichment as an effective P supply to wheat. Plant Soil 2010, 327:347-354.
26. Shanbhag A.G. Utilization of information measure as a means of image thresholding. Graph. Models Image Process. 1994, 56:414-419.
27. Suralta R.R., Yamauchi A. Root growth, aerenchyma development, and oxygen transport in rice genotypes subjected to drought and waterlogging. Environ. Exp. Bot. 2008, 64:75-82.
28. Tanaka S., Yamauchi S., Kono S. Easily accessible method for root length measurement using an image analysis system. Jpn. J. Crop Sci. 1995, 64:144-147.
29. Tsai W. Moment-preserving thresholding: a new approach. Comput. Vis. Graph. Image Process. 1985, 29:377-393.
30. Yen J.C., Chang F.J., Chang S. A new criterion for automatic multilevel thresholding. IEEE Trans. Image Process. 1995, 4:370-378.
31. Zack G.W., Rogers W.E., Latt S.A. Automatic measurement of sister chromatid exchange frequency. J. Histochem. Cytochem. 1977, 25:741-753.
32. Zobel R.W. Sensitivity analysis of computer-based diameter measurement from digital images. Crop Sci. 2003, 43:583-591.