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Analysis of form and function using integrated high-throughput open-source workflows

Venue: Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany

Date: 28.10.19 – 1.11.19

Information about the workshop: Large scale studies of shape and function have provided considerable insight into patterns and causes of biological diversification at the phenotypic level. For example, beak shapes of more than 97% of the ex­­tant genera of birds (>2,000 species) have been analysed in a single study using highly automated analysis routines (Cooney et al. 2017). Despite these efforts, more options for highly (semi-)automated analyses of variations in shape and function are needed in order to analyse the immense data quantities generated by high-throughput imaging applications such as microCT, CLSM, etc. and to cope with the immense diversity of even more speciose taxa.

This workshop aims to present options for an integrated methodological pipeline to analyse aspects of shape and function for hundreds of specimens in a reasonable timeframe. In particular, we will focus on the analysis of shape variation using geometric morphometrics (GM) and the analysis of functional aspects using finite element analysis (FEA). The analysis of GM data requires the placement of landmarks which means that the workshop will start with this data collection step and its prerequisites including best practice examples. Different options for the generation of 2D and 3D data, the efficient placement of landmarks and their analysis will be presented using a combination of IMAGEJ, BLENDER, and the R software environment.

The part of the workshop about FEA will cover the generation of the raw data, FEA setup, and analysis of the results. A particular focus will be placed on the prerequisites for physiologically meaningful FEA setups such as options for the measurement of material parameters and the correct application of physiological boundary conditions which reflect the biological problem. Simulations will be carried out using an open-source FE-solver and the results will be analysed using the R and PARAVIEW software environments.

As a special guest, Dr. Stephan Lautenschlager (University of Birmingham, UK) kindly agreed to add his expertise concerning 3D modelling and analysis to this workshop. Check out his beautiful work @https://stephanlautenschlager.com/

Prospective workshop participants are encouraged to bring their own datasets so that potential analysis types or problems can be discussed on site.

Because it can be expected that more people are interested in the workshop than we will be able to handle, an application, including your CV and a one page (or less) motivation letter should be sent to a.blankeSpamProtectionuni-koeln.de no later than June 30th 2019. Please include a short comment, whether you intend to bring an own dataset for analysis (This will not influence the decision for attendance, it is only intended for informative purposes). Final decisions regarding the participation will be communicated four weeks later. No participation fee will be charged. Board and accommodation are at your own expenses. Depending on the composition of the participant group the workshop will be held in English or German.

References

  • Cooney C.R., Bright J.A., Capp E.J.R., Chira A.M., Hughes E.C., Moody C.J.A., Nouri L.O., Varley Z.K., Thomas G.H. 2017. Mega-evolutionary dynamics of the adaptive radiation of birds. Nature. 542:344–347.