"Morphos"

  • Datum: 16.12.15

  • Morphology and Morphometrics

Morphology & Anatomy

  • Gilles Carpentier Research Web Site: Computer Image Analysis

    • Image analysis tools in biology and biochemistry using ImageJ
    • E.g. Scale Bar Tools for Microscopes
      The "Scale Bar Tools for Microscopes" allows drawing of scale bars in image margins, for several microscopes profiles stored on the computer. It also allows calibration of images, and keeps set informations in metadata. The integrity of the image area is so preserved, and margins can be removed by a single click.

Morphometrics

Background

  1. Jensen, J.R., Ciofani, M.K. & Miramontes, C.L., 2002. Lines, Outlines, and Landmarks: Morphometric Analysis of Leaves of Acer rubrum, Acer saccharinum (Aceraceae) and Their Hybrids. Taxon, 51(3), pp.475–492.
    Available at: http://www.jstor.org/stable/1554860.
  2. Kuhl, F.P. & Giardina, C.R., 1982. Elliptic Fourier features of a closed contour. Computer graphics and image processing, 18(3), pp.236–258.
    Available at: http://www.sciencedirect.com/science/article/pii/0146664X8290034X.
  3. Dryden, I.L. & Mardia, K. V, 1998. Statistical shape analysis, Wiley Chichester.
  4. Stegmann, M.B.B. & Gomez, D.D.D., 2002. A brief introduction to statistical shape analysis. Informatics and Mathematical, (March), pp.1–15.
    Available at: http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_shape_spaces_imm403.pdf.

Software - Forms

  1. Iwata, H. & Ukai, Y., 2002. SHAPE: A Computer Program Package for Quantitative Evaluation of Biological Shapes Based on Elliptic Fourier Descriptors. Journal of Heredity, 93(5), pp.384–385.
    Available at: http://jhered.oxfordjournals.org/content/93/5/384.short.
    • Es handelt sich hierbei um ein Programm zur Analyse von geschlossenen Konturen.
    • Die im Paper angegebene URL, welche zum Programm Download führen sollte, funktioniert nicht. Über eine Google Suche nach "SHAPE Iwata" gelangt man aber zur derzeitigen Web Seite auf der man das Programm runter laden kann.
  2. Klingenberg, C.P., 2011. MorphoJ: An integrated software package for geometric morphometrics. Molecular Ecology Resources, 11(2), pp.353–357.
    Available at: http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2010.02924.x/full.
    • Eine umfangreiche auf Java basierte Sammlung von Werkzeugen für die Auswertung von Morphometrischen Daten. Neben einer Downloadmöglichkeit findet man auf der Homepage auch eine umfangreiche Anleitung.
    • Klingenberg, C.P., 2008. Morphological Integration and Developmental Modularity. Annual Review of Ecology, Evolution, and Systematics, 39(1), pp.115–132.
      Available at: http://www.jstor.org/stable/30245156.
    • Klingenberg, C.P., 2009. Morphometric integration and modularity in configurations of landmarks: Tools for evaluating a priori hypotheses. Evolution and Development, 11(4), pp.405–421.
      Available at: http://www.onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2009.00347.x/full.
    • Klingenberg, C.P. & Leamy, L.J., 2001. Quantitative genetics of geometric shape in the mouse mandible. Evolution; international journal of organic evolution, 55(11), pp.2342–2352.
      Available at: http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2001.tb00747.x/abstract.
    • Lande, R., 1979. Quantitative Genetic Analysis of Multivariate Evolution, Applied to Brain: Body Size Allometry. Evolution, 33(1), pp.pp. 402–416.
      Available at: http://www.jstor.org/stable/2407630.
    • Klingenberg, C.P., Barluenga, M. & Meyer, A., 2002. Shape Analysis Of Symmetric Structures: Quantifying Variation Among Individuals And Asymmetry. Evolution, 56(10), pp.1909–1920.
      Available at: http://dx.doi.org/10.1111/j.0014-3820.2002.tb00117.x.
    • Klingenberg, C.P. & McIntyre, G.S., 1998. Geometric Morphometrics of Developmental Instability: Analyzing Patterns of Fluctuating Asymmetry with Procrustes Methods. Evolution, 52(5), pp.pp. 1363–1375.
      Available at: http://www.jstor.org/stable/2411306.

Software - Seeds

  1. Tanabata, T. et al., 2012. SmartGrain: High-throughput phenotyping software for measuring seed shape through image analysis. Plant Physiology, 160(December), pp.1871–1880.
    Available at: http://www.plantphysiol.org/content/160/4/1871.full.

  2. Whan, A.P. et al., 2014. GrainScan: a low cost, fast method for grain size and colour measurements. Plant Methods, 10(1), p.23.
    Available at: http://www.plantmethods.com/content/10/1/23.

  3. Moore, C.R. et al., 2013. Mapping quantitative trait loci affecting Arabidopsis thaliana seed morphology features extracted computationally from images. G3, 3(1), pp.109–118.
    Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3538336.

  4. Brewer, M.T. et al., 2006. Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species. Plant physiology, 141(1), pp.15–25.
    Available at: http://www.plantphysiol.org/content/141/1/15.short.
    Rodríguez, G.R. et al., 2010. Tomato Analyzer: a useful software application to collect accurate and detailed morphological and colorimetric data from two-dimensional objects. Journal of visualized experiments : JoVE, (37), pp.1–9.
    Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146067/.

Software - Leaves

  1. Backhaus, A. et al., 2010. leafprocessor: a new leaf phenotyping tool using contour bending energy and shape cluster analysis. New Phytologist, 187(1), pp.251–261.
    Available at: http://dx.doi.org/10.1111/j.1469-8137.2010.03266.x.
    • Die im Paper angegebene URL, welche zum Programm Download führen sollte, funktioniert nicht. Backhaus ist mittlerweile nicht mehr in Sheffield. Auf der Internetseite seiner neuen Stelle findet man zwar Informationen zum LeafProcessor aber keine Möglichkeit zum Download. Wer das Tool dennoch ausprobieren will, darf sich mit Herrn Backhaus in Verbindung setzen.
  2. Bylesjö, M. et al., 2008. LAMINA: a tool for rapid quantification of leaf size and shape parameters. BMC Plant Biology, 8(1), p.82.
    Available at: http://www.biomedcentral.com/1471-2229/8/82.
    • Programm basiert auf JAVA und benötigt das Java Advanced Imaging (JAI) package. Dieses ist laut Angaben der Programmierer im Download enthalten und muss nicht separat installiert werden.
    • Download der Software (Java) über SourceForge.
  3. Maloof, J.N. et al., 2013. LeafJ: An ImageJ plugin for semi-automated leaf shape measurement. JoVE (Journal of Visualized Experiments), (71), pp.e50028–e50028.
    Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582691/.
    • Download der Software (ImageJ plugin) über BitBucket.
    • Den Video Artikel findet man bei Jove. Um ihn komplett anschauen zu können muss man sich einen Trial Account (= 10 Minuten Zeit) besorgen, da das KIT (noch) kein Abo hat.
  4. Weight, C., Parnham, D. & Waites, R., 2008. TECHNICAL ADVANCE: LeafAnalyser: a computational method for rapid and large-scale analyses of leaf shape variation. The Plant Journal, 53(3), pp.578–586.
    Available at: http://dx.doi.org/10.1111/j.1365-313X.2007.03330.x.
    • Die im Paper angegebene URL, welche zum Programm Download führen sollte, funktioniert nicht. Es hat den Anschein, als wäre die Seite gehackt worden. Man findet das Programm aber bei SourceForge!