How to 3D Print a Micro-CT Scan

3D printing and X-ray micro-CT 3D imaging are obvious partners. 3D printing has become an affordable, mainstream technology. This post walks you through the process from scanning, reconstructing and binarising through meshing to 3D printing.

There are many useful, real-world applications for micro-CT and 3D printing, including:

Here are the key steps of how to 3D print a micro-CT scan. A method note is available with more detailed information – please get in touch if you’d like a copy. Blue Scientific is the official UK supplier for the full range of Bruker micro-CT scanners, from entry-level scanners to highly advanced systems, and we are available to advise on the best scanner for your research:

 Contact us on 01223 422 269 or

 View the range of Micro-CT Scanners

How to 3D Print a Micro-CT Scan

1) Scan and Reconstruct

Control program + NRecon

The first step is the usual micro-CT scanning process. Scan the object as normal; It’s recommended not to choose the smallest pixel size, but the optimal one for the sample. In this case, more pixels generate larger datasets and models, and not necessarily better results.

X-ray micro-CT image

Maximum intensity projection of the reconstructed slices

2) Binarise


If the resolution of the scan is higher than required for the part to be printed, the dataset should be resized. Thresholding should then be carried out as usual. Image filters can be useful when thresholding. Next, the ROI (Region of Interest) is defined.

It is advisable to remove potential noise from the image, using despeckling and/or morphological tools in the software. This can have a great effect on the file size of the final 3D model.

3) Meshing


A 3D model representing the surface of the binary object needs to be constructed. Typically this consists of polygonal elements (in this case triangles – see below) of which the vertices and normals are saved.

CTAnalyser (Bruker 3D data analysis software) outputs in commonly used 3D file types, including .stl and .ply. Check which file type is best for the 3D printer that you’ll be using.

Close-up of the ribs, showing the triangular mesh

Close-up of the ribs, showing the triangular mesh

4) Inspection


Before printing, inspect the mesh using CTVol, a surface rendering programme. Check that any thin structures are preserved well. For some models it may be necessary to repeat the binarisation and meshing steps.

Micro-CT surface render

Surface render of the micro-CT model, using Bruker CTVol

5) 3D Printing

Import the model into the 3D printer software and rescale to the required size. Depending on the type of printer and its resolution, the printed parts may need to be cleaned and/or finished.

 Contact us on 01223 422 269 or

 View Micro-CT Scanners

3D print made from a micro-CT scan

Final 3D print, created from the original micro-CT image