00X-RAYS OF OBJECTS, NOT PEOPLE

Free the fossil,
leave the rock.

A fossil ammonite half embedded in a block of grey limestone resting on a plain laboratory bench in soft side light — AI-generated image, not a photograph of a real person or place.

Some fossils never leave their stone.

Micro-CT lets scientists see a fossil inside its rock without chipping a grain away. A museum worked example shows how a shark tooth about 315 million years old was scanned, sliced and freed on screen.

X-RAYfrom every angleUpdated 18 October 2026

Time a scan

01Principles

Turn it through 360°
Slice it on screen
Lift it from the rock
Non-destructive, start to finish

02THE SHORT ANSWER

Thousands of X-rays,
one 3D fossil.

CT measures how much X-ray gets through.
Software turns those views into slices you can explore.

INSIDE THE ROCK

Non-destructive by design

The Natural History Museum describes micro-CT as a non-invasive and non-destructive way to make 3D models of the inside and outside of specimens.

Time a scan

THE SCAN

A turntable and a beam

The fossil turns through 360° in a cone of X-rays while a detector records a radiograph every 0.05° to 0.1°, mapping how much X-ray passes through.

How slices are made

VIRTUAL PREPARATION

Separating fossil from matrix

On screen, voxels are sorted by grey value into rock, tooth tissue and empty canals, so the fossil can be lifted out digitally.

The steps

03A QUICK TIME CHECK

Where does
the time go?

Pick a stage of making a virtual fossil. The bar shows how long it takes in the worked example, from the scan itself to preparing the fossil on screen.

Based on Abel, Laurini and Richter (2012), Palaeontologia Electronica, a micro-CT workflow using a Natural History Museum fossil shark tooth.

Time check

Choose a stageCollecting the CT scanExpert preparing the toothBeginner preparing the toothA difficult specimen

Collecting the CT scan15 to 120 minutes

The time to collect the original CT volume varies with the system. The authors say scanning is no longer the main limit.

Expert preparing the toothAbout 4 hours

The shark tooth has a fairly simple structure, so an expert can prepare it virtually in around four hours.

Beginner preparing the tooth16 to 40 hours

A beginner needs roughly 16 to 40 hours for the same tooth, which is why the paper calls data processing the main limiting factor.

A difficult specimenUp to 40 hours

The authors say difficult specimens can take 40 hours to process, far longer than the scan that produced them.

Source: Abel, Laurini and Richter (2012), A palaeobiologist's guide to 'virtual' micro-CT preparation, Palaeontologia Electronica 15(2).

04TWO NUMBERS WORTH KNOWING

Tiny cubes,
finer than a hair.

How small each 3D pixel was for the shark tooth,
and how big the detector that caught the X-rays.

0.009 mm

Size of each 3D pixel in the scan

The effective spatial resolution was 0.050 mm or coarser, because resolution is usually two to five times the voxel size. The best voxel size is about 1/2000th of the fossil's width or height.

VOXEL SIZE · SHARK TOOTH

2,000 × 2,000

Pixels across the detector panel

Each row of detector pixels becomes one slice. The tooth was scanned at 180 kV and 138 µA; a larger or denser fossil would need higher settings.

DETECTOR · MICRO-CT

Source: Abel, Laurini and Richter (2012). The fossil is Sphenacanthus hybodoides, a freshwater shark from Longton, Staffordshire, that lived about 315 million years ago.

05FROM SCAN TO VIRTUAL FOSSIL

Four stages
on the computer.

The paper sets out a ten-step workflow. Grouped together, it comes down to four jobs after the scan.

Clean up the slices
Reduce noise, which makes scans grainy, and correct beam hardening, which makes the edges of a dense fossil look brighter than its centre.
Stretch the contrast
Spread the fossil's grey values so that tooth tissue and rock are easier to tell apart.
Segment the fossil
Use a threshold, a region-growing tool and a mask to separate the fossil from the rock matrix around it.
Render and store
Light and false-colour the model, animate it, then archive the slice stack so other researchers can use it.

A fossil fish preserved in a split slab of dark shale lying on a pale table, its fine bones still partly hidden in the stone — AI-generated image, not a photograph of a real person or place.

06HOW SLICES ARE MADE

Tomography means
writing in slices.

A small dark fossil tooth in a chip of rock fixed upright on a small round sample stage, with blurred metal equipment behind — AI-generated image, not a photograph of a real person or place.

The word comes from the Greek tomos (slice) and graphein (to write). Software lines up the radiographs like the spokes of a bicycle wheel and back-projects them, smearing them across each other to build each slice from voxels, or 3D pixels.

Each voxel's grey value reflects how strongly the material absorbs X-rays, which depends mostly on density but also on thickness and atomic number. Allan Cormack and Godfrey Hounsfield shared the 1979 Nobel Prize for developing computer assisted tomography.

07Questions

Questions people ask

What is micro-CT?

It is X-ray computed tomography at a fine scale. The Natural History Museum describes it as a non-invasive, non-destructive technique that uses X-rays to create 3D models of the internal and external features of specimens.

Does CT scanning damage a fossil?

CT is described as non-destructive: the fossil is X-rayed, not cut. Racicot (2017) adds that a scan becomes a lasting digital record that can be shared with researchers, museums and the public.

Why can the edge of a fossil look brighter than its middle?

That is beam hardening. The X-ray beam mixes energies, and lower-energy X-rays are absorbed first, so the beam gets more penetrating as it passes through. A copper filter or later software correction can reduce it.

What limits how fine the detail can be?

Mainly voxel size. Features smaller than a voxel can blur or disappear, and at very small voxel sizes noise becomes the limit. The fossil must fill the detector for the best magnification.

Where was the first CT system used?

Abel and colleagues note that the first system, developed by Godfrey Hounsfield and Allan Cormack, went online in 1972 at Atkinson Morley's Hospital in London. The same principle is used for fossils today.

08Sources

Free the fossil,
leave the rock.