Skip to main content Accessibility help
×
Home

Automated leaf physiognomic character identification from digital images

  • Norman MacLeod (a1) (a2) (a3) and David Steart (a4)

Abstract

Research into the relationship between leaf form and climate over the last century has revealed that, in many species, the sizes and shapes of leaf characters exhibit highly structured and predictable patterns of variation in response to the local climate. Several procedures have been developed that quantify covariation between the relative abundance of plant character states and the states of climate variables as a means of estimating paleoclimate parameters. One of the most widely used of these is the Climate Leaf Analysis Multivariate Program (CLAMP). The consistency, accuracy and reliability with which leaf characters can be identified and assigned to CLAMP character-state categories is critical to the accuracy of all CLAMP analyses. Here we report results of a series of performance tests for an image-based, fully automated at the point of use, leaf character scoring system that can be used to generate CLAMP leaf character state data for: leaf bases (acute, cordate and round), leaf apices (acute, attenuate), leaf shapes (ovate, elliptical and obovate), leaf lobing (unlobed, lobed), and leaf aspect ratios (length/width). This image-based system returned jackknifed identification accuracy ratios of between 87% and 100%. These results demonstrate that automated image-based identification systems have the potential to improve paleoenvironmental inferences via the provision of accurate, consistent and rapid CLAMP leaf-character identifications. More generally, our results provide strong support for the feasibility of using fully automated, image-based morphometric procedures to address the general problem of morphological character-state identification.

Copyright

References

Hide All
Bailey, I. W., and Sinnott, E. W.. 1915. A botanical index of Cretaceous and Tertiary climates. Science 41:831834.
Bailey, I. W., and Sinnott, E. W.. 1916. The climatic distribution of certain types of angiosperm leaves. American Journal of Botany 3:2439.
Belman, R. 1961. Adaptive control processes: a guided tour. Princeton University Press, Princeton.
Clark, J. Y., Corney, D. P. A., and Tang, H. L.. 2012. Automated plant identification using artificial neural networks. Pp. 342–348. 2012 IEEE Symposium on computational intelligence in bioinformatics and computational biology (CIBCB). IEEE, San Diego, California.
Colquhoun, W. P. 1959. The effect of a short rest pause on inspection efficiency. Ergonomics 2:367372.
Colquhoun, W. P 1982. Biological rhythms and performance. Pp. 5986In W. B. Webb, ed. Biological rhythms, sleep, and performance. Wiley, Cichester.
Cope, J. S., Corney, D., Clark, J. Y., Remagnino, P., and Wilkin, P.. 2012. Plant species identification using digital morphometrics: a review. Expert Systems with Applications 39:75627573.
Corney, D. P. A., Tang, H. L., Clark, J. Y., Hu, Y., and Jin, J.. 2012a. Automating digital leaf measurement: The tooth, the whole tooth, and nothing but the tooth. PLoS One. Public Library of Science.
Corney, D. P. A., Clark, J. Y., Tang, H. L., and Wilkin, P.. 2012b. Automatic extraction of leaf characters from herbarium specimens. Taxon 61:231244.
Culverhouse, P. F., MacLeod, N., Williams, R., Benfield, M. C., Lopes, R. M., and Picheral, M.. 2013. An empirical assessment of the consistency of taxonomic identifications. Marine Biology Research 10(1), 7384.
Culverhouse, P. F., Williams, R., Reguera, B., Herry, V., and González-Gil, S.. 2003. Do experts make mistakes? A comparison of human and machine identification of dinoflagellates. Marine Ecology Progress Series 247:1725.
Culverhouse, P. F. R., MacLeod, N., Williams, R., Benfield, M. C., Lopes, R. M., and Picheral, M.. 2013. An empirical assessment of the consistency of taxonomic identifications. Marine Biology Research 10:7384.
Evans, J. S. B. T. 1987. Bias in human reasoning: causes and consequences. Laurence Erlbuam Associates, Hove.
Fox, J. G. 1971. Background music and industrial efficiency — a review. Applied Ergonomics June, 7073.
Ginsburg, R. N. 1997a. An attempt to resolve the controversy over the end-Cretaceous extinction of planktic foraminifera at El Kef, Tunisia using a blind test. Introduction: background and procedures. Marine Micropaleontology 29:6768.
Ginsburg, R. N 1997b. Perspectives on the blind test. Marine Micropaleontology 29:101103.
Godfrey-Smith, P. 2003. Theory and reality: an introduction to the philosophy of science. University of Chicago Press, Chicago, Ill., London.
Gregory-Wodzicki, K. M. 2000. Relationships between leaf morphology and climate, Bolivia: implications for estimating paleoclimate from fossil floras. Paleobiology 26:668688.
Huff, P. M., Wilf, P., and Azumah, E. J.. 2003. Digital Future for paleoclimate estimation from fossil leaves? Preliminary results. Palaios 18(3), 266274.
Jacques, F. M. B., Sub, T., Spicer, R. A., Xing, Y., Huang, Y., Wanga, W., and Zhoub, Z.. 2011. Leaf physiognomy and climate: Are monsoon systems different? Global and Planetary Change 76:5662.
Kaesler, R. L. 1993. A window of opportunity: peering into a new century of paleontology. Journal of Paleontology 67:329333.
Kovach, W. L., and Spicer, R. A.. 1996. Canonical correspondence analysis of leaf physiognomy:a contribution to the development of a new palaeoclimatological tool. Palaeoclimates 2:125138.
MacLeod, N. 2002a. Geometric morphometrics and geological form-classification systems. Earth-Science Reviews 59:2747.
MacLeod, N 2002b. Phylogenetic signals in morphometric data. Pp. 100138. In N. MacLeod, and P. L. Forey, eds. Morphology, shape and phylogeny. Taylor & Francis, London.
MacLeod, N 2005. Shape models as a basis for morphological analysis in paleobiological systematics: dicotyledonous leaf physiography. Bulletins of American Paleontology 369:219238.
MacLeod, N 2007. Automated taxon identification in systematics: theory, approaches, and applications. CRC Press, Taylor & Francis Group, London.
MacLeod, N——. 2015. The direct analysis of digital images (eigenimage) with a comment on the use of discriminant analysis in morphometrics. Pp. 156–182. In P. E. Lestrel, ed. Proceedings of the Third International Symposium on Biological Shape Analysis. World Scientific, Singapore.
MacLeod, N., Benfield, M., and Culverhouse, P. F.. 2010. Time to automate identification. Nature 467:154155.
MacLeod, N., Krieger, J., and Jones, K. E.. 2013. Geometric morphometric approaches to acoustic signal analysis in mammalian biology. Hystrix 24:116125.
Manly, B. F. J. 1994. Multivariate statistical methods: a primer. Chapman & Hall, Bury, St. Edmonds, Suffolk.
Manly, B. F. J 1997. Randomization, bootstrap and Monte Carlo methods in biology. Chapman Hall, London.
Mitteröcker, P., and Bookstein, F. L.. 2011. Linear discrimination, ordination, and the visualization of selection gradients in modern morphometrics. Evolutionary Biology 38:100114.
Royer, D. L., Wilf, P., Janesko, D. A., Kowalski, E. A., and Dilcher, D. L.. 2005. Correlations of climate and plant ecology to leaf size and shape: potential proxies for the fossil record. American Journal of Botany 92:11411151.
Royer, D. L., Peppe, D. J., Wheeler, E. A., and Niinemets, U.. 2012. Roles of climate and functional traits in controlling toothed vs. untoothed leaf margins. American Journal of Botany 99(5), 915922.
Sokal, R. R. 1974. Classification: purposes, principles, progress, prospects. Science 185:11151123.
Spicer, R. A. 2000. Leaf physiognomy and climate change. Pp. 244264. In C. S., and R. P., eds. Biotic Response to Global change: the Last 145 Million Years. Cambridge University Press, Cambridge, U.K.
Spicer, R. A 2008. CLAMP. Pp. 156158. In V. Gornitz, ed. Encyclopedia of paleoclimatology and ancient environments. Dordrecht, Germany.
Spicer, R. A., Bera, S., De Bera, S., Spicer, T. E. V., Srivastava, G., Mehrotra, R., Mehrotra, N., and Yang, J.. 2011. Why do foliar physiognomic climate estimates sometimes differ from those observed? Insights from taphonomic information loss and a CLAMP case study from the Ganges Delta. Palaeogeography, Palaeoclimatology, Palaeoecology 302(3–4):381395.
Spicer, R. A., Valdes, P. J., Spicer, T. E. V., Craggs, H. J., Srivastava, G., Mehrotra, R. C., and Yang, J.. 2009. New developments in CLAMP: calibration using global gridded meteorological data. Palaeogeography, Palaeoclimatology, Palaeoecology 283:9198.
Spicer, R. A., Valdes, P. J., Spicer, T. E. V., Craggs, H. J., Srivastava, G., Mehrotra, R. C., and Yang, J.. 2010. Quantification of uncertainties in fossil leaf paleoaltimetry: Does leaf size matter? Tectonics 29(6), TC6001.
Spicer, R. A., and Yang, J.. 2010. Quantification of uncertainties in fossil leaf paleoaltimetry: Does leaf size matter? Tectonics 29(6):TC6001.
Steart, D. C., Spicer, R. A., and Bamford, M. K.. 2010. Is southern Africa different? An investigation of the relationship between leaf physiognomy and climate in southern African mesic vegetation. Review of Palaeobotany and Palynology 162:607620.
Su, T., Xing, Y.-W., Liu, Y.-S., Jacques, F. M. B., Chen, W.-Y., Huang, Y.-J., and Zhou, Z.-K.. 2010. Leaf margin analysis: a new equation from humid to mesic forests in China. Palaios 25:234238.
Sykes, B., Mullis, R. J., Hagenmuller, C., Melton, T., and Sartori, M.. 2014. Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates. Proceedings of the Royal Society B: Biological Sciences 281(1789):10.1098/rspb.2014.0161.
Weimann, M. C., Manchester, S. R., Dilcher, D. L., Hinojosa, L. F., and Wheeler, E. A.. 1998. Estimation of temperature and precipitation from morphological characters of dicotyledonous leaves. American Journal of Botany 85:17961802. Biological Sciences.
Wilf, P. 1997. When are leaves good thermometers? A new case for leaf margin analysis. Paleobiology 23:373390.
Wilf, P., Wing, S. L., Greenwood, D. R., and Greenwood, C. L.. 1998. Using fossil leaves as paleoprecipitation indicators: an Eocene example. Geology 26:203206.
Wolfe, J. A. 1995. Paleoclimatic estimates from Tertiary leaf assemblages. Annual Review of Earth and Planetary Science 23:119142.
Wolfe, J. A., and Upchurch, G. R.. 1987. North American nonmarine climates and vegetation during the Late Cretaceous. Palaeogeography, Palaeoclimatology, Palaeoecology 61:3377.
Zachariasse, W. J., Riedel, W. R., Sanfilippo, A., Schmidt, R. R., Brolsma, M. J., Schrader, H. J., Gersonde, R., Drooger, M. M., and Brokeman, J. A.. 1978. Micropaleontological counting methods and techniques — an exercise on an eight meters section of the Lower Pliocene of Capo Rossello, Sicily. Utrecht Micropaleontological Bulletins 17:1265.
Zimek, A., Schubert, E., and Kriegel, H.-P.. 2012. A survey on unsupervised outlier detection in high-dimensional numerical data. Statistical Analysis and Data Mining 5(5), 363387.

Related content

Powered by UNSILO

Automated leaf physiognomic character identification from digital images

  • Norman MacLeod (a1) (a2) (a3) and David Steart (a4)

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed.