D4.4 - Micro-computed tomography for natural history specimens: Handbook of best practice protocols


1. Scope and structure of this handbook
2. The image acquisition workflow
3. Protocols for micro-CT image acquisition
  3.1 Pre-scan considerations and specimen preparation
     3.1.1 Zoological specimens
     3.1.2 Botanical specimens
     3.1.3 Paleontological specimens
     3.1.4 Geological specimens
  3.2 Scanning containers and scanning mediums
  3.3 Scanning process
     3.3.1 Calibrating the system
     3.3.2 Placing the specimen
     3.3.3 Setting up the detector parameters
  3.4. Reconstruction
  3.5 Visualisation and post-processing
  3.6 Troubleshooting
4. Use cases
  4.1 Zoological samples
  4.2. Botanical samples
  4.3. Palaeontological samples
  4.4 Geological (mineral) samples
5. Data curation
  5.1 Metadata
  5.2 Data organisation, storage and archival
  5.3 Data dissemination and publication
6. References
7. Glossary of terms
8. Appendix
  8.1 List of institutions with micro-CT
  8.2 List of microCT manufacturers
  8.3 List of softwares

Project element: 
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith