1. Sarah Faulwetter, Katerina Vasileiadou, Michalis Kouratoras, Thanos Dailianis, Gordon Paterson, Daniel Sykes, Christos Arvanitidis Micro-computed tomography as a tool for the 21st century taxonomist? An evaluation using polychaetes.

2. micro-tomography x-ray source Rotating sample detector 3. micro-tomography x-ray source Rotating sample detector Density-based (no true colours) Highest resolution: ~0.8m / pixel (SEM: 1-20nm) Visualises internal and external structures Non-destructive 4. image acquisition projection images 1. scanning 5. image acquisition projection images cross-sections 1. scanning 2. reconstruction 6. image acquisition projection images cross-sections 1. scanning three-dimensional volume rendering 3. visualisation 2. reconstruction 7. the idea Source: http://www.naturkundemuseum-berlin.de/typo3temp/pics/d09e9f46e0.jpg type material 8. cybertype the idea Source: http://www.naturkundemuseum-berlin.de/typo3temp/pics/d09e9f46e0.jpg type material Godfray, HCJ (2007) Linnaeus in the information age. Nature 446: 259260 9. requirements A cybertype should... 10. ... provide morphological and anatomical information of the same accuracy and reliability as the physical type material ... be linked to the original type material, which can be consulted if in doubt. ... be retrievable be created without affecting the morphological, anatomical and molecular identity of the physical specimen requirements A cybertype should... 11. ... provide morphological and anatomical information of the same accuracy and reliability as the physical type material ... be linked to the original type material, which can be consulted if in doubt ... be retrievable be created without affecting the morphological, anatomical and molecular identity of the physical specimen requirements A cybertype should... 12. requirements ... provide morphological and anatomical information of the same accuracy and reliability as the physical type material ... be linked to the original type material, which can be consulted if in doubt be created without affecting the morphological, anatomical and molecular identity of the physical specimen A cybertype should... 13. requirements ... provide morphological and anatomical information of the same accuracy and reliability as the physical type material ... be linked to the original type material, which can be consulted if in doubt be created without affecting the morphological, anatomical and molecular identity of the physical specimen ... be retrievable A cybertype should... 14. aims of the study to assess the potential of micro-computed tomography to create digital morphological and anatomical data for taxonomic studies. 15. aims of the study to assess the potential of micro-computed tomography to create digital morphological and anatomical data for taxonomic studies. to evaluate whether the digital representations comply with the requirements for the cybertype concept. 16. methods 9 polychaete specimens were scanned and examined 17. Discrimination of characters (a) external features Phyllodoce lineata 18. Alitta succinea & Syllis gracilis Discrimination of characters (a) external features 19. Scanning Electron Microscope (SEM) Micro-CT Source: Aguado et al. 2008, Zootaxa Microscopic features of the chaetae lack detail with micro-CT Discrimination of characters (a) external features 20. Alitta succinea Discrimination of characters (b) internal features 21. Lumbrineris latreilli Light microscope and drawing Micro-CT (re-modelled) Discrimination of characters (b) internal features 22. conclusions Examination of morphological characters in their natural position Non-destructive examination of internal features without dissection Isolation of morphological features and individual examination Truly three-dimensional investigation and analysis Models can be included in interactive taxonomic publications (pdf) Strengths of the technique 23. conclusions Limitations of the technique Image resolution in the range of 0.8 to 100 m/pixel Outperformed by electron or optical microscopy Inability to detect true colours in specimens Effects of ionizing radiation on DNA not yet fully known Creation of high-resolution models is time-consuming 24. conclusions Is micro-CT ready to provide cybertypes for taxonomy? 25. conclusions Is micro-CT ready to provide cybertypes for taxonomy? Not quite yet... 26. conclusions Is micro-CT ready to provide cybertypes for taxonomy? Not quite yet... ...but certainly it is the way to go! 27. conclusions Is micro-CT ready to provide cybertypes for taxonomy? Not quite yet... ...but certainly it is the way to go! Technological progress is still required (resolution, scanning speed, storage archives, data transfer, ... ) Standards for proper curation and documentation of 3D-types should be developed (by museums and IT community) Adoption from the taxonomic community is needed 28. conclusions Adoption from the taxonomic community is needed From the taxonomic triangle ... 29. conclusions Adoption from the taxonomic community is needed to the taxonomic tetrahedron? description type cybertype name 30. conclusions to the taxonomic tetrahedron? description type cybertype name Adoption from the ICZN is needed 31. outlook and there's the potential for more... 32. outlook Sources: http://www.isgtw.org/sites/default/files/img_2011/BinaryToDNA.jpg http://wp.streetwise.co/wp-content/uploads/2012/08/293940-5847-5-300x225.jpeg genOMICS transcriptOMICS proteOMICS 33. outlook Sources: http://www.isgtw.org/sites/default/files/img_2011/BinaryToDNA.jpg http://wp.streetwise.co/wp-content/uploads/2012/08/293940-5847-5-300x225.jpeg vs. conventional taxonomy Source: http://www.mnh.si.edu/rc/cp/collPhotoGallery.htm genOMICS transcriptOMICS proteOMICS 34. outlook Sources: http://www.isgtw.org/sites/default/files/img_2011/BinaryToDNA.jpg http://wp.streetwise.co/wp-content/uploads/2012/08/293940-5847-5-300x225.jpeg genOMICS transcriptOMICS proteOMICS vs. conventional taxonomy Source: http://www.mnh.si.edu/rc/cp/collPhotoGallery.htm Big data ? high-tech / digital analogue 35. outlook what if... 36. we used the cross-sections along the body... outlook 37. outlook we used the cross-sections along the body... 38. outlook we used the cross-sections along the body... 39. outlook we used the cross-sections along the body... 40. converted them to density (greyscale) values... outlook 41. from which similarity matrices can be calculated... outlook 42. and compared... Spearman's correlation outlook 43. and compared... Spearman's correlation 2nd stage similarity matrix outlook 44. and compared... 2nd stage similarity matrix Information on how morphological/anatomical patterns change along the organism outlook 45. and compared... 2nd stage similarity matrix Information on how morphological/anatomical patterns change along the organism phenetic profile of the organism outlook 46. and compared... 2nd stage similarity matrix Information on how morphological/anatomical patterns change along the organism phenetic profile of the organism + mass digitizations & algorithms Phenomics outlook 47. just be creative ! and if you want even more ...