If you are publishing on CT data generated by someone else, here are some recommendations on how to report the correct information in your paper…

A note: if you intend to publish on CT data created by somebody else, it’s always a good idea to communicate with the creator of that data. They will be your best source of information on how the data were generated!

1. Cite the original publication

If the data were originally published in a peer-reviewed paper, make sure to cite the paper when you first introduce the data (usually in the “methods” section). Publications may be:

Accompanying publication/preprint to a collection or database of scans. Examples include:

• The open Vertebrate project: Blackburn et al. 2024 https://doi.org/10.1093/biosci/biad12 
• OzBoneViz: Weisbecker et al. 2024 https://doi.org/10.1101/2024.12.04.626889

Publications describing specific scans. Examples include:

• Stewart et al. 2023: The axial skeleton of Tiktaalik roseae https://doi.org/10.1073/pnas.2316106121 
• Iwaniuk et al. 2020: The endocast of the Night Parrot (Pezoporus occidentalis) reveals insights into its sensory ecology and the evolution of nocturnality in birds https://doi.org/10.1038/s41598-020-65156-0

If there is no associated publication (i.e. scans were downloaded from a repository and have not been published on before), often there will be an identifying project or media number for your scans that you can mention in the text. 

2. Report scanning parameters

Scanning and reconstruction parameters can often be found in the text or supplemental files of the original manuscript, or on the media page in the data repository used by the original author. If you have trouble finding the scanning and reconstruction parameters, contact the author of the study, or the person who generated the scans, and ask them for the appropriate information. 

If you only included several scans in your research, you can report the scanning parameters in the text. Here’s an example from Gray et al (2023), describing four scans in total (skeletal and diceCT scans of two species):

“All micro-CT scanning was conducted at the Nanoscale Research Facility at the University of Florida using a General Electric Phoenix v|tome|x m 240 (General Electric/Waygate Technologies, Boston, MA, USA). Skeletal scans were performed at 100 kV (Kinosternon) and 140 kV (Gopherus) with 200 μA (Kinosternon) and 220 μA (Gopherus), with 200 ms exposure timing, 3× frame averaging with a skip of 1, a 0.1 mm Cu filter, and voxel sizes of 42.6 (Kinosternon) and 54.69 (Gopherus). DiceCT scans were performed for both at 150 kV with 200 μA, with 200 ms exposure timing, 3× frame averaging with a skip of 1, a 0.5 mm Cu filter. The voxel sizes were 44.95 (Kinosternon) and 56.98 microns (Gopherus).”

 If your research includes many scans, it will make more sense to include a table in your supplemental material with the details of your scanning parameters. If you choose this option, you might also like to report the range of parameters used in the text of your “methods” section. You can use the NoCTURN terminology resource to help you report parameters correctly. Here’s a list of information and parameters to include in your table:

• Scanning facility (include RRID/ROR if possible)
• CT scanner used and type of X-ray tube
• Specimen information – for natural history specimens, include the institution, collection, and catalog number of the specimens scanned (Darwin Core Triplet e.g. for a herpetological specimen at the Florida Museum – UF:herp:123456). If possible, link up to the specimen record in iDigbio. 
• Scanning mode/imaging trajectory – some scanners have different modes including regular volume scans, helical scans (translates the rotating turntable vertically across the detector field while gathering X-ray projections), mosaic scans (shifts the detectors to acquire objects larger than the detector field of view). 
• Voltage (usually reported in kV)
• Current (usually reported in uA)
• Exposure timing (usually reported in ms)
• Filter used – whether a filter was used, and if so, the material (typically Aluminum or Copper) and the filter thickness.
• Gain/sensitivity – units vary by scanner manufacturer
• Frame averaging (also report if frames were “skipped”)
• Binning
• Voxel size (usually reported in microns)
• Any physical filters used
• Contrast enhancing treatment applied to the specimen – staining agent used, concentration, staining duration.

3. Report reconstruction parameters

Reconstruction is an important part of the CT scanning process. If possible, please report the following:

• Reconstruction software and version used
• Center shift value
• Beam hardening correction
• Smoothing
• Histogram calibrations performed

4. Acknowledge the right people, facility and funding sources

In your acknowledgements section, please thank the authors of the study the scans were first published in, and the facility (include RRID/ROR if possible) and the person who generated the scan with their ORCID (they may not always be listed as an author). Include the grant numbers that funded the scans. 

To find out who generated a scan, you can ask the corresponding author of the original publication. If you downloaded a scan from MorphoSource, you can also find the scan “creator” under the IMAGE ACQUISITION AND PROCESSING IN DETAIL section of the media page. If no name is listed, contact the “data manager” (listed under OWNERSHIP AND PERMISSIONS).