A Computer Program Package for Quantitative Evaluation of Biological Shapes
Based on Elliptic Fourier Descriptors
A free program for biological shape analyses!
Why was gSHAPEh developed?
Quantitative evaluation of the shapes of biological organs is often required in various research fields, such as agronomy, medicine, genetics, ecology and taxonomy. Elliptic Fourier descriptors (EFDs) (Kuhl and Giardina 1982) can delineate any type of shape with a closed two-dimensional contour, and have been effectively applied to the evaluation of various biological shapes in animals and plants. Quantization of shapes is a prerequisite for evaluating the inheritance of morphological traits in quantitative genetics (e.g. Iwata et al. 2004a; Iwata et al. 2004b; Uga et al. 2003; Iwata et al. 2002a; Iwata et al. 2002b; Iwata et al. 2000; Iwata et al. 1998). However, quantization of shapes is not easy for a general researcher.
What is gSHAPEh?
I developed the program package named SHAPE for general application of the method based on EFDs. SHAPE extracts the contour shape from a full color bitmap image, delineates the contour shape with the EFDs, and finally performs the principal component analysis of the EFDs for summarizing the shape information. With the aid of this package, a researcher can easily analyze shapes on a personal computer without special knowledge about the procedures related to the method. For more details about SHAPE, please see Iwata and Ukai (2002).
! Caution If you have been a user of the older version of SHAPE, please beware of the following point:
I found a bug in SHAPE ver.1.2, which has been fixed in SHAPE ver.1.3. Because of this bug, chain-code obtained by SHAPE ver.1.2 traces an object's contour "clockwise", although it is expected to trace a contour "counter-clockwise" in general (You can check the direction of contour trace by viewer programs, ChcVeiwer and NefViewer). EFDs derived from clockwise chain-code are different from ones derived from counter-clockwise code in the sign of coefficients b and d. As indicated in Table 1, the difference in the sign of the coefficients may not cause any serious problem in the shape analyses, if all EFD or chain-code data are obtained by the same version of SHAPE. However, it should cause a serious artifact, if you analyze jointly the data obtained by the different version of SHAPE. Please be sure NEVER TO ANALYZE JOINTLY EFD or chain-code data obtained by THE DIFFERENT VERSION OF SHAPE! For the joint analysis, please use converter programs to convert the direction of contour trace of chain-code or EFDs obtained by SHAPE ver.1.2. I greatly apologize for the inconvenience.
Table 1. Direction of contour trace and problems in shape analyses
|EFD and chain-code Data||Direction of contour trace||Problems in shape analyses||Ways of coping|
|Data obtained by SHAPE ver.1.2||Clockwise||No problem||Not necessary|
|Data obtained by SHAPE ver.1.3||Counter-clockwise||Of course, No problem||Not necessary|
|Combined data obtained by both versions||The mixture of clockwise and contour-clockwise||The difference in the direction of contour trace causes the difference in the sign of Fourier coefficients b and d. This should cause a serious artifact in the analyses||Use converter programs before analyzing the conbined data|
How can you use gSHAPEh?
SHAPE is a free ware. However, please cite Iwata and Ukai (2002) when you intend to publish results analyzed with SHAPE. SHAPE can be run on any IBM compatible computer under Windows 95, 98, NT or higher versions. The program package and a related on-line manual can be downloaded from the following links.
SHAPE (shape.zip, 3,892KB)
This is a complete package of SHAPE, which includes all the files listed below.
Program package (shape_s.zip, 2,194KB)
Samples (sample.zip, 662KB)
Manual (PDF version) manual.pdf, 461KB)
Manual (Shockwave Flash version) (manual.swf, 233KB)
Tutorial (PDF version) (tutorial.pdf, 804KB)
Tutorial (Shockwave Flash version) (tutorial.swf, 572KB)
After downloading, please install SHAPE as follows.
@Correspondence to me
Hiroyoshi IWATA (Ph.D)
Laboratory of Biometry and Bioinformatics,
Departiment of Agricultural and Environmental Biology,
Graduate School of Agricultural and Life Sciences
The University of Tokyo
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, JAPAN
Tel: +81-3-5841-5069; Fax: +81-3-5841-5069
Web page: http://lbm.ab.a.u-tokyo.ac.jp/~iwata
|Iwata, H., and Y. Ukai (2002) SHAPE: A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity 93: 384-385.|
|Iwata, H., S. Niikura, S. Matsuura, Y. takano and Y. Ukai (2004a) Interaction between genetic effects and soil type in diallel analysis of root shape and size of Japanese radish (Raphanus sativus L.). Breeding Science 54: 313-318. <Abstract> <PDF>|
|Iwata, H., S. Niikura, S. Matsuura, Y. takano and Y. Ukai (2004b) Genetic control of root shape at different growth stages in radish (Raphanus sativus L.). Breeding Science 54: 117-124. <Abstract> <PDF>|
|Uga, Y., Y. Fukuta, H. W. Cai, H. Iwata, R. Ohsawa, H. Morishima and T. Fujimura (2003) Mapping QTLs influencing rice floral morphology using recombinant inbred lines derived from a cross between Oryza sativa L. and O. rufipogon Griff. Theoretical and Applied Genetics 107: 218-226.|
|Iwata, H., H. Nesumi, S. Ninomiya, Y. Takano and Y. Ukai (2002a) The evaluation of genotype x environment interactions of citrus leaf morphology using image analysis and elliptic Fourier descriptors. Breeding Science 52: 243-251. <Abstract> <PDF>|
|Iwata, H., H. Nesumi, S. Ninomiya, Y. Takano and Y. Ukai (2002b) Diallel analysis of leaf shape variations of citrus varieties based on elliptic Fourier descriptors. Breeding Science 52: 89-94. <Abstract> <PDF>|
|Iwata, H., S. Niikura, S. Matsuura, Y. Takano and Y. Ukai (2000) Diallel analysis of root shape of Japanese radish (Raphanus sativus L.) based on elliptic Fourier descriptors. Breeding Science 50: 73-80.|
|Iwata, H., S. Niikura, S. Matsuura, Y. Takano and Y. Ukai (1998) Evaluation of variation of root shape of Japanese radish (Raphanus sativus L.) based on image analysis using elliptic Fourier descriptors. Euphytica 102: 143-149.|
|Kuhl, F. P., and C. R. Giardina (1982)
Elliptic Fourier features of a closed contour. Computer Graphics and
Image Processing 18: 236-258.