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Semi-automatic landmark point annotation for geometric morphometrics


Schunke,  Anja C.
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

Tautz,  Diethard
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Bromiley, P. A., Schunke, A. C., Ragheb, H., Thacker, N. A., & Tautz, D. (2014). Semi-automatic landmark point annotation for geometric morphometrics. Frontiers in Zoology, 11: 61. doi:10.1186/s12983-014-0061-1.

BACKGROUND: In previous work, the authors described a software package for the digitisation of 3D landmarks for use in geometric morphometrics. In this paper, we describe extensions to this software that allow semi-automatic localisation of 3D landmarks, given a database of manually annotated training images. Multi-stage registration was applied to align image patches from the database to a query image, and the results from multiple database images were combined using an array-based voting scheme. The software automatically highlights points that have been located with low confidence, allowing manual correction. RESULTS: Evaluation was performed on micro-CT images of rodent skulls for which two independent sets of manual landmark annotations had been performed. This allowed assessment of landmark accuracy in terms of both the distance between manual and automatic annotations, and the repeatability of manual and automatic annotation. Automatic annotation attained accuracies equivalent to those achievable through manual annotation by an expert for 87.5% of the points, with significantly higher repeatability. CONCLUSIONS: Whilst user input was required to produce the training data and in a final error correction stage, the software was capable of reducing the number of manual annotations required in a typical landmark identification process using 3D data by a factor of ten, potentially allowing much larger data sets to be annotated and thus increasing the statistical power of the results from subsequent processing e.g. Procrustes/principal component analysis. The software is freely available, under the GNU General Public Licence, from our web-site (