Sarah Faulwetter, Katerina Vasileiadou, Michalis Kouratoras,
Thanos Dailianis, Gordon Paterson, Daniel Sykes, Christos Arv...
micro-tomography
x-ray source
Rotating sample
detector
micro-tomography
x-ray source
Rotating sample
detector
● Density-based (no true colours)
● Highest resolution: ~0.8μm / pi...
image acquisition
projection images
1. scanning
image acquisition
projection images cross-sections
1. scanning 2. reconstruction
image acquisition
projection images cross-sections
1. scanning
three-dimensional
volume rendering
3. visualisation
2. reco...
the idea
Source: http://www.naturkundemuseum-berlin.de/typo3temp/pics/d09e9f46e0.jpg
type material
cybertype
the idea
Source: http://www.naturkundemuseum-berlin.de/typo3temp/pics/d09e9f46e0.jpg
type material
Godfray, HCJ ...
requirements
A cybertype should...
... provide morphological and anatomical information of the same
accuracy and reliability as the physical type material
.....
... provide morphological and anatomical information of the same
accuracy and reliability as the physical type material
.....
requirements
... provide morphological and anatomical information of the same
accuracy and reliability as the physical typ...
requirements
... provide morphological and anatomical information of the same
accuracy and reliability as the physical typ...
aims of the study
… to assess the potential of micro-computed tomography to
create digital morphological and anatomical da...
aims of the study
… to assess the potential of micro-computed tomography to
create digital morphological and anatomical da...
methods
9 polychaete specimens were scanned and examined
Discrimination of characters –
(a) external features
Phyllodoce lineata
Alitta succinea & Syllis gracilis
Discrimination of characters –
(a) external features
Scanning Electron Microscope (SEM) Micro-CT
Source: Aguado et al. 2008, Zootaxa
Microscopic features of the chaetae lack d...
Alitta succinea
Discrimination of characters –
(b) internal features
Lumbrineris latreilli
Light microscope and drawing Micro-CT (re-modelled)
Discrimination of characters –
(b) internal feat...
conclusions
● Examination of morphological characters in their natural position
● Non-destructive examination of internal ...
conclusions
Limitations of the technique
● Image resolution in the range of 0.8 to 100 μm/pixel
● Outperformed by electron...
conclusions
Is micro-CT ready to provide cybertypes for taxonomy?
conclusions
Is micro-CT ready to provide cybertypes for taxonomy?
Not quite yet...
conclusions
Is micro-CT ready to provide cybertypes for taxonomy?
Not quite yet...
...but certainly it is the way to go!
conclusions
Is micro-CT ready to provide cybertypes for taxonomy?
Not quite yet...
...but certainly it is the way to go!
•...
conclusions
Adoption from the taxonomic community is needed
From the “taxonomic triangle” ...
conclusions
Adoption from the taxonomic community is needed
… to the “taxonomic tetrahedron”?
description
type
cybertype
n...
conclusions
… to the “taxonomic tetrahedron”?
description
type
cybertype
name
Adoption from the ICZN is needed
outlook
… and there's the potential for more...
outlook
Sources: http://www.isgtw.org/sites/default/files/img_2011/BinaryToDNA.jpg
http://wp.streetwise.co/wp-content/uplo...
outlook
Sources: http://www.isgtw.org/sites/default/files/img_2011/BinaryToDNA.jpg
http://wp.streetwise.co/wp-content/uplo...
outlook
Sources: http://www.isgtw.org/sites/default/files/img_2011/BinaryToDNA.jpg
http://wp.streetwise.co/wp-content/uplo...
outlook
what if...
… we used the cross-sections along the body...
outlook
outlook
… we used the cross-sections along the body...
outlook
… we used the cross-sections along the body...
outlook
… we used the cross-sections along the body...
… converted them to density (greyscale) values...
outlook
… from which similarity matrices can be calculated...
outlook
… and compared...
Spearman's correlation
ρ
ρ
ρ
outlook
… and compared...
Spearman's correlation
ρ
ρ
ρ
2nd
stage similarity matrix
outlook
… and compared...
2nd
stage similarity matrix
Information on how
morphological/anatomical patterns
change along the organi...
… and compared...
2nd
stage similarity matrix
Information on how
morphological/anatomical patterns
change along the organi...
… and compared...
2nd
stage similarity matrix
Information on how
morphological/anatomical patterns
change along the organi...
… just be creative !
… and if you want even more ...
Micro-CT as a tool for cybertaxonomists
Micro-CT as a tool for cybertaxonomists
Micro-CT as a tool for cybertaxonomists
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Micro-CT as a tool for cybertaxonomists

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Is micro-computed tomography a suitable tool for the modern taxonomist? An example using polychaetes. Presented by Christos Arvanitidis at the 13th International Polychaete Conference, August 2013, Sydney

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Micro-CT as a tool for cybertaxonomists

  1. 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. 2. micro-tomography x-ray source Rotating sample detector
  3. 3. micro-tomography x-ray source Rotating sample detector ● Density-based (no true colours) ● Highest resolution: ~0.8μm / pixel (SEM: 1-20nm) ● Visualises internal and external structures ● Non-destructive
  4. 4. image acquisition projection images 1. scanning
  5. 5. image acquisition projection images cross-sections 1. scanning 2. reconstruction
  6. 6. image acquisition projection images cross-sections 1. scanning three-dimensional volume rendering 3. visualisation 2. reconstruction
  7. 7. the idea Source: http://www.naturkundemuseum-berlin.de/typo3temp/pics/d09e9f46e0.jpg type material
  8. 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: 259–260
  9. 9. requirements A cybertype should...
  10. 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. 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. 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. 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. 14. aims of the study … to assess the potential of micro-computed tomography to create digital morphological and anatomical data for taxonomic studies.
  15. 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. 16. methods 9 polychaete specimens were scanned and examined
  17. 17. Discrimination of characters – (a) external features Phyllodoce lineata
  18. 18. Alitta succinea & Syllis gracilis Discrimination of characters – (a) external features
  19. 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. 20. Alitta succinea Discrimination of characters – (b) internal features
  21. 21. Lumbrineris latreilli Light microscope and drawing Micro-CT (re-modelled) Discrimination of characters – (b) internal features
  22. 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. 23. conclusions Limitations of the technique ● Image resolution in the range of 0.8 to 100 μm/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. 24. conclusions Is micro-CT ready to provide cybertypes for taxonomy?
  25. 25. conclusions Is micro-CT ready to provide cybertypes for taxonomy? Not quite yet...
  26. 26. conclusions Is micro-CT ready to provide cybertypes for taxonomy? Not quite yet... ...but certainly it is the way to go!
  27. 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. 28. conclusions Adoption from the taxonomic community is needed From the “taxonomic triangle” ...
  29. 29. conclusions Adoption from the taxonomic community is needed … to the “taxonomic tetrahedron”? description type cybertype name
  30. 30. conclusions … to the “taxonomic tetrahedron”? description type cybertype name Adoption from the ICZN is needed
  31. 31. outlook … and there's the potential for more...
  32. 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. 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. 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. 35. outlook what if...
  36. 36. … we used the cross-sections along the body... outlook
  37. 37. outlook … we used the cross-sections along the body...
  38. 38. outlook … we used the cross-sections along the body...
  39. 39. outlook … we used the cross-sections along the body...
  40. 40. … converted them to density (greyscale) values... outlook
  41. 41. … from which similarity matrices can be calculated... outlook
  42. 42. … and compared... Spearman's correlation ρ ρ ρ outlook
  43. 43. … and compared... Spearman's correlation ρ ρ ρ 2nd stage similarity matrix outlook
  44. 44. … and compared... 2nd stage similarity matrix Information on how morphological/anatomical patterns change along the organism outlook
  45. 45. … and compared... 2nd stage similarity matrix Information on how morphological/anatomical patterns change along the organism “phenetic profile” of the organism outlook
  46. 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. 47. … just be creative ! … and if you want even more ...

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