Ctagent

The paraffin-embedded lung samples were scanned using a custom-built Nikon Metrology micro-CT scanner at an isotropic voxel size of 8 μm as previously described (24 (link)), with optimization to maximize soft tissue contrast. An X-ray tube potential peak of 55 kVp was used at a beam current of 104 to 114 μA. 2,601 tomographic radiographic viewpoints of the samples were assessed (360° rotation in 0.14° steps) by acquiring 64 repeated projections (2,000 × 2,000 pixels) for each angular step to increase signal-to-noise ratio through frame averaging, where integration time for individual projections was set to 500 ms at an isotropic voxel size of 8 μm, resulting in a field of view of 16 × 16 mm². Together with sample shuttling during acquisition to suppress ring artefacts with the reconstruction, the gross image acquisition time per sample was about 24 hours. The projections were then reconstructed in 3D using the Feldkamp, Davis, and Kress algorithm for cone beam tomography in the DigiR3D tomography reconstruction module of the DigiXCT software suite (Digisens) or using standard filtered-back projection within CTPro3D (v. XT 2.2 service pack 10, Nikon Metrology) and CTAgent (v. XT 2.2 service pack 10, Nikon Metrology) (35 (link)).

Projection data were reconstructed as 32‐bit float raw volumes with an isotropic voxel size using filtered back‐projection algorithms implemented in CT Pro 3D and CT Agent software (v. XT 2.2 SP10, Nikon Metrology, UK). Voxel dimensions were 103.3 μm³ for IWCMS 2014.95.1, 89.3 μm³ for IWCMS 2014.95.2, and 109.7 μm³ for IWCMS 2014.95.3. These were converted to 8‐bit (raw) volume files to reduce computational load.
To improve contrast, the raw image files of the basicranium fragment (IWCMS 2014.95.3) were manipulated in FIJI (Schindelin et al., 2012 (link)) using the “sharpen” filter and background subtract function. Additional sharpening of the Ceratosuchops braincase material was conducted within Object Research Systems (ORS) Dragonfly (v. 2022.1, build 1249) via the Unsharp filter (Workflow > Image Filtering > Operations > Sharpening) using a factor of 4–9 (standard deviation = 1), depending on the specimen/region of interest (ROI).