A CT scan arrives as a stack of greyscale images, often hundreds of them. A 3D printer needs a closed surface model, usually an STL file. Segmentation is the work that turns one into the other. Here is what happens at each stage.
Step 1: Receiving the DICOM data
Medical scans are stored in DICOM format. Each file is one slice through the body and carries information about pixel spacing and slice thickness, which is what lets software rebuild the scan at true scale. For printing, the full series is needed rather than exported screenshots. Thinner slices generally give smoother, more accurate models.
Before data is shared, it should be handled in line with the hospital’s data protection procedures, for example by removing patient-identifying details where they aren’t needed.
Step 2: Isolating the anatomy
Every pixel in a CT image has a value in Hounsfield units, a measure of how strongly that tissue absorbs X-rays. Bone sits much higher on the scale than soft tissue, so a first pass often uses thresholding: selecting every pixel within a chosen range.
Thresholding alone is rarely enough. Neighbouring bones touch, contrast agents can look like bone, and thin structures may fall outside the range. The engineer refines the selection slice by slice: separating structures, filling gaps and removing anything that isn’t part of the region of interest.
Step 3: Building the 3D surface
Once the region is defined in every slice, software stacks the slices and generates a 3D surface mesh around it. The raw mesh is usually rough, showing a “staircase” effect between slices, along with small floating fragments and holes.
Step 4: Cleaning and preparing for print
- Smoothing removes slice artefacts without changing clinically meaningful shape.
- Repairing closes holes and removes loose fragments so the model is a watertight solid.
- Separating parts lets structures be printed in different colours or materials, or taken apart.
- Adding supports or bases where needed, such as a stand for a skull or connectors between pieces.
The finished model is checked against the original scan to confirm nothing important was lost or added along the way.
Step 5: Printing and finishing
The prepared file is printed at the required scale and detail, then cleaned, has its support material removed and is inspected. The material is chosen for the model’s purpose: durable for repeated handling in teaching, or finely detailed for planning.
What to send us: the full DICOM series for the area of interest, a note on what the model is for, and any deadline. We’ll review the data and confirm what’s achievable before quoting.
Why the process matters
Most of the accuracy in an anatomical model is decided before printing even starts, in the segmentation. That’s why we treat it as engineering work, with checks at each step. Learn more about our medical 3D printing service or read why hospitals use printed models.