TABLE 1. Samples investigated in this study using micro-CT. For the first time, such a large set of more than 60 specimens from nine different materials was investigated using this technique.
| Case studies | Material | Age | Country | Locality |
| 1 | Internal moulds of invertebrate body fossils preserved in the siliceous nodules | Middle Ordovician | Czechia | Díly, Rokycany, Praha-Šárka, Osek |
| 2 | Bryozoan colony of/in marls to clayey limestones | Middle Ordovician | Russia | Khrevitsa-St. Petersburg Region |
| 3 | Epibiontic interactions of bryozoan colonies and conulariid specimens from clayey limestones | Upper Ordovician | Czechia | Loděnice |
| 4 | Apatitic periderm of conulariids | Upper Ordovician | Czechia | Praha-Libeň, Praha-Palmovka, Vráž, Loděnice |
| 5 | Calcareous shells of platycerid gastropods from organodetritic limestones | Lower Devonian | Czechia | Koněprusy |
| 6 | Peloidal grainstone | Middle Devonian | Czechia | Eifelian, ensensis conodont Zone, Jirásek quarry, Koněprusy area |
| 7 | Calcitic or calcitic/aragonitic serpulid tube worms | Upper Cretaceous | France | Gazonfier/Yvré-l'Évêque, Le Mans region |
| 8 | Organic-walled egg-like bodies in lacustrine sediments | uppermost Pleistocene | Czechia | Stará Jímka core |
| 9 | Recent calcareous large foraminifers from Posidonia oceanica seagrass meadows | Recent | Malta | Mediterranean Sea |
TABLE 2. Suggested settings of micro-CT for selected types of material. Comments for the respective columns: Filter: The x-ray beam energy can be modified using different beam filters. Voltage source and current: Specimens with lesser or greater x-ray permeability require adjusting the energy of the x-rays. The x-ray beam energy can be modified by altering voltage to the tube. Increasing voltage also means decreasing current. Random movement: Very small, regular movements of specimens help to compensate for mechanical inaccuracies in micro-CT. Rotation step: The rotation step determines how much the sample rotates between images.
| Case studies | Type of material | Filter | Specimen size | Voltage source/current source | Random movement | Rotation step (degree) |
Image pixel size (μm) |
| 1 | Internal moulds of siliceous nodules | Cu 1 mm | 1–5 cm | 100 kV/120-124 μA | 10 | 0.2 | 3–13 |
| 2 | Marls to clayey limestones | Cu 1 mm | 5 cm | 100 kV/100 μA | 10 | 0.3 | 27.08 μm |
| 3 | Clayey limestones | Cu 1 mm | 3–5 cm | 100 kV/100 μA | 1 | 0.2 | 13.5 |
| 4 | Apatitic periderm | Al 0.5 mm | 3–10 mm | 49–80 kV /124–200 μA | 1–5 | 0.2 –0.22 | 2.06–2.84 |
| 5 | Organodetritic limestones | Al + Cu | 3–5 mm | 80–100 kV/100–124 μA | 2 | 0.2 | 0.95–2.34 |
| 6 | Limestone | Cu 1 mm | 0.5 cm | 100 kV/100 μA | 5 | 0.2 | 1.08 |
| 7 | Calcitic or calcitic/aragonitic serpulid tube worms | Al 0.5 mm | 1–2 cm | 80 kV/124 μA | 10 | 0.2 | 4 |
| 8 | Organic-walled egg-like bodies | no filter | 0.2 mm | 40 kV/250 μA | 0 | 0.2 | 0.54 |
| 9 | Foraminifers | Al 0.25 mm | 1.5 mm | 59 kV/167 μA | 5 | 0.2 | 1 |
TABLE 3. Glossary. Explanation of terms used in the present paper.
| 3D data sets | The final result of a CT scan. It is a product of dedicated software processing called tomographic reconstruction. It is a 3D voxel-based model of the scanned object. A 3D dataset is typically stored and used as a set of digital images representing virtual cross-sections of the scanned object. |
| Avizo | Software application which enables users to perform interactive visualization and computation on 3D data sets. |
| Bioerosion | Destruction and removal of a consolidated mineral or lithic substrate by the direct action of organisms. |
| Filter | The x-ray beam energy can be modified using different beam-filters. There are two basic filters in the Skyscan 1172 tomograph built into the device. Besides the default setting (no filter), there is a 0.5 mm aluminium filter and a combined 1 mm copper + aluminium filter. However, the majority of our studied fossil materials required the use of additional custom–made filters, because of a low x-ray permeability of the samples. |
| Ortho-slice | Techniques of visualization and computer graphics creating slices through the x, y, and z planes. |
| Oversize scan and off-set mode | For large samples, Oversize scans, in some cases in combination with Off-set mode were used. This functionality of the SkyScan 1172 allows automatic imaging of the sample in two or more sections sequentially, and their subsequent merging during the reconstruction process into a single volume. |
| Random movement | Very small, regular moving of specimen helping in compensation of mechanical inaccuracies in micro-CT. |
| Rotation step | The rotation step (measured in degrees) determines how much the sample rotates between images. |
| Segmentation | Segmentation assigns a label to each part of the image that belongs to the material under investigation. The aim of segmentation is to display the selected inner part of the object (the most common are, for example, the internal organs of animals). The images from the 3D dataset are scrolled step by step, and each image is manually colored. |
| Scanning process | Comprises all steps when the object is inside an x-ray device. |
| Tomographic reconstruction | A set of dedicated mathematical algorithms creating 3D model of the scanned object using a set of acquired 2D x-ray images. |
| Voltage source/current | Specimens of lower or higher x-ray density require the adjustment of energy of the x-rays. The x-ray beam energy can be modified by varying voltage to the tube. Selective removing of the low x-rays energy beams by filters increases mean x-ray beam energy. For each filter, a suitable voltage value is recommended. Increasing voltage decreases current and vice versa. |
| Volume rendering | A set of techniques in scientific visualization and computer graphics, used to display an object from the 3D data set. |
| Voxel | Voxel is the smallest building block of 3D digital data. It is a volumetric equivalent of an image pixel. Unlike a pixel, voxel has three usually isotropic dimensions and can be, therefore, understood as a small cube providing information on a certain position in a 3D space. |
| X-ray image | Two-dimensional shadow images of three-dimensional structures produced by x-ray. |
TABLE 4. Overview of the selected types of materials investigated in this study.
| Case studies | Sample/lithology | Host organism/substrate | Infilling of borings/ burrows/ material of epibionts | Specimen size | Invertebrate tracemakers | Ichnotaxa | Size of studied structures | Number of studied samples |
| 1 | Siliceous nodules of the Šárka Formation | Internal moulds of invertebrates | Empty | 1–5 cm | Unknown organisms (?Polychaeta) | Arachnostega Pilichnus Palaeophycus |
0.5 –3 mm | 29 |
| 2 | Marls to clayey limestones | Bryozoan colony | Light-grey clayey limestone (same as the specimen) | 5 cm | clionaid sponges | Entobia cf.devonica | 2.5 mm–1 cm | 1 |
| 3 | Clayey limestones | Conulariid walls (apatite) of Archaeoconularia fecunda | Clayey limestones | 3–5 cm | Epizoic bryozoans | Not determined | 3–5 cm | 3 |
| 4 | Apatitic periderm | Fragments of conulariid periderm | Empty or filled by siltstone | 3–10 mm | Unknown organism | Not determined | 5–20 µm | 4 |
| 5 | Organodetritic limestones | Fragments of platycerid gastropod shells | Empty or filled by organodetritic limestone | 3–5 mm | Unknown organism | Not determined | 5–20 µm | 3 |
| 6 | Limestone | Sparite | Sparitic calcite | 0.5 cm | Cyanobacteria, Fungi | Not determined | 30 µm | 1 |
| 7 | Calcitic or calcitic/aragonitic | Serpulid tube worms Pyrgopolon (Pyrgopolon) deforme | Empty | 1–2 cm | Barnacles, clionaid sponges,polychaetes, sipunculans | Rogerella, Entobia, Trypanites, Maeandropolydora | 100 µm | 15 |
| 8 | Siltstone | Organic-walled egg-like bodies presumed chitin composition | Empty | 0.2 mm | Probable endoliths belonged to Fungi | Not determined | 1 µm | 3 |
| 9 | Calcite | Foraminifers Sorites | Empty | 1.5 mm | Probably green algae, cyanobacteria or perhaps also fungi | Not determined | 10 µm | 3 |
