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A New Method for Morphometric Analysis of Opal Phytoliths from Plants

  • Welmoed A. Out (a1), José F. Pertusa Grau (a2) and Marco Madella (a3)


Micro-morphometry has substantially gained ground in the field of phytolith analysis, but the comparability of results is limited due to the use of different methods. This paper presents a new, user-friendly method based on open-source software (FIJI) that is proposed as a step towards the introduction of a standard method. After obtaining a mask of a phytolith by making a digital drawing, 27 commonly used variables of size and shape are measured automatically. This method is not only useful for phytolith analysis, but may also be used for other fields of morphometric research. Users can furthermore customize the software tool when additional variables are required.


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Albert, R.M., Bamford, M.K. & Cabanes, D. (2009). Palaeoecological significance of palms at Olduvai Gorge, Tanzania, based on phytolith remains. Quat Int 193, 4148.
Ball, T.B. & Brotherson, J.D. (1992). The effect of varying environmental conditons on phytolith morphometries in two species of grass (Bouteloua curtipendula and Panicum virgatum). Scanning Microsc Int 6(4), 11631181.
Ball, T.B., Ehlers, R. & Standing, M.D. (2009). Review of typologic and morphometric analysis of phytoliths produced by wheat and barley. Breed Sci 59, 505512.
Ball, T., Gardner, J.S. & Brotherson, J.D. (1996). Identifying phytoliths produced by the inflorescence bracts of three species of wheat (Triticum monococcum L., T. dicoccon Schrank., and T. aestivum L.) using computer-assisted image and statistical analysis. J Archaeol Sci 23, 619632.
Ball, T.L. (1992). Note on preparing stained phytolith assemblages. The Phytolitharian Newsletter 7(2), 67.
Bretz, F., Hothorn, T. & Westfall, P. (2011). Multiple Comparisons using R. London: Chapman and Hall/CRC.
Brown, D.A. (1984). Prospects and limits of a phytolith key for grasses in the central United States. J Archaeol Sci 11, 345368.
Burns, R.P. & Burns, R. (2009). Business Research Methods and Statistics using SPSS. London: Sage.
Dayanandan, P., Kaufman, P.B. & Franklin, C.I. (1983). Detection of silica in plants. Am J Bot 70, 10791084.
Dougherty, B. (2005). Measure ROI curve. Version 1 2/26/2007 (2007). Update with using the new version of the Custom Particle Analyzer by G. Joss and W. Rasband. Available at (retrieved 1 March 2014).
Fuller, D., Stevens, C. & McClatchie, M. (2014). Routine activities, tertiary refuse and labor organization: social inference from everyday Archaeobotany. In Ancient Plants and People. Contemporary Trends in Archaeobotany, Madella, M., Lancelotti, C. & Savard, M. (Eds.). Tucson: University of Arizona Press.
Grubben, G.J.H. & Partohardjono, S. (1996). Plant Resources of South-East Asia. Volume 10: Cereals. Bogor: Prosea Foundation.
Gu, Y., Zhao, Z. & Pearsall, D.M. (2013). Phytolith morphology research on wild and domesticated rice species in East Asia. Quat Int 287, 141148.
IBM Corp. (2012). IBM SPSS Statistics for Windows, Version 21.0. Armonk, New York: IBM Corp.
Iriarte, J. (2003). Assessing the feasibility of identifying maize through the analysis of cross-shaped size and three-dimensional morphology of phytoliths in the grasslands of southeastern South America. J Archaeol Sci 30, 10851094.
Laird, N.M. & Ware, J.H. (1982). Random-effects models for longitudinal data. Biometrics 38(4), 63974.
Landini, G. (2013). Particles_8. Version 2.12 14/Sep/2010. Available at (retrieved 1 March 2014).
Lu, H. & Liu, K.-B. (2003). Morphological variations of lobate phytoliths from grasses in China and the south-eastern United States. Divers Distrib 9, 7387.
Lu, H., Zhang, J., Wu, N., Liu, K.-B. & Xu, D. (2009). Phytoliths analysis for the discrimination of foxtail millet (Setaria italica) and common millet (Panicum miliaceum). PLoS One 4(2), e4448. doi: 10.1371/journal.pone.0004448.
Madella, M., Lancelotti, C. & García-Granero, J.J. (2013). Millet microremains – an alternative approach to understand cultivation and use of critical crops in prehistory. Archaeol Anthropol Sci. doi: 10.1007/s12520-013-0130-y.
Madella, M. & Zurro, D. (2009). Phytoliths. In Archaeobotanical Online Tutorial , Charles, M., Crowther, A., Ertug, F., Herbig, C., Jones, G., Kutterer, J., Longford, C., Madella, M., Maier, U., Out, W., Pessin, H. & Zurro, D. (Eds.). University of Sheffield. Available at (retrieved 1 March 2014).
Metcalfe, C.R. (1960). Anatomy of the Monocotyledons Gramineae. Oxford: Clarendon Press.
Mulholland, S.C. & Rapp, G.R. (1992). Phytolith systematics: an introduction. In Phytolith Systematics: Emerging Issues, Rapp, G.R. & Mullholland, S.C. (Eds.), pp. 113. New York: Plenum Press.
Pearsall, D.M. (1978). Phytolith analysis of archeological soils: evidence for maize cultivation in formative Ecuador. Science 199, 177178.
Piperno, D.R. (1984). A comparison and differentiation of phytoliths from maize (Zea mays L.) and wild grasses: use of morphological criteria. Am Antiq 49, 361383.
Piperno, D.R. (2006). Phytoliths: A Comprehensive Guide for Archaeologists and Paleoecologists. Lanham: AltaMira Press.
Piperno, D.R. (2009). Identifying crop plants with phytoliths (and starch grains) in Central and South America: a review and an update of the evidence. Quat Int 193, 146159.
Powers, A.H. (1992). Great expectations: a short historical review of european phytolith systematic. In Phytolith Systematics: Emerging Issues, Rapp, G.R. & Mullholland, S.C. (Eds.), pp. 1535. New York: Plenum Press.
R Core Team. (2013). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing. Available at (retrieved 1 March 2014).
Rasband, W.S. (1997–2012). ImageJ, U.S. National Institutes of Health, Bethesda, Maryland, USA, (retrieved 1 March 2014).
Rovner, I. & Russ, J.C. (1992). Darwin and design in phytolith systematics: morphometric methods for mitigating redundancy. In Phytolith Systematics: Emerging Issues, Rapp, G.R. & Mullholland, S.C. (Eds.), pp. 253276. New York: Plenum Press.
Schaarschmidt, F. & Vaas, L. (2009). Analysis of trials with complex treatment structure using multiple contrast tests. HortScience 44(1), 188195.
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J.-Y., James White, D., Hartenstein, V., Eliceiri, V., Tomancak, P. & Cardona, A. (2012). Fiji: an open-source platform for biological image-analysis. Nat Methods 9(7), 676682.
Shillito, L.-M. (2013). Grains of truth or transparent blindfolds? A review of current debates in archaeological phytolith analysis. Veg Hist Archaeobot 22(1), 7182.
Verbeke, G. & Molenberghs, G. (2000). Linear Mixed Models for Longitudinal Data. New York: Springer.
Zhao, Z., Pearsall, D.M., Benfer, R.A. Jr. & Piperno, R. (1998). Distinguishing rice (Oryza sativa Poaceae) from wild oryza species through phytolith analysis, II: finalized method. Econ Bot 52(2), 134145.
Zohary, D., Hopf, M. & Weiss, E. (2012). Domestication of Plants in the Old World. Oxford: Oxford University Press.


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A New Method for Morphometric Analysis of Opal Phytoliths from Plants

  • Welmoed A. Out (a1), José F. Pertusa Grau (a2) and Marco Madella (a3)


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