3D SLicer

Generating Scientific 3D Models

By Alejandro Romero


3D Slicer is an open-source program that allows for the three-dimensional visualization and processing of CT scans. The steps to go from a raw CT image sequence to a segmented 3D mesh are outlined below.

Preparing the Image Data

Total time: ~10 min

Morphosource is a great place to find sequences of CT scan images if you do not already have a dataset.

To import your images into 3D Slicer, you will need an .nrrd file. If you do not already have an existing .nrrd file, you can generate one using Fiji, a free image processing package available here: https://fiji.sc/

Generating an NRRD File

Generating 3D Model

Using 3D Slicer

    4. In Volumes, set Image Spacing to the dimensions of the original image sequence, which can usually be found in a metadata file. If using         a scan from MorphoSource, the dimensions are listed in the specimen scan description.

    5.  You should now have a workspace that looks like this:

You can adjust your workspace in: View → Layout (Conventional is the layout option used in the visuals provided here).

Next, let’s generate a 3D mesh:

To export your mesh, click on the Segmentations icon.

5. You now have a segmented 3D mesh! However, final mesh changes (e.g. polygon reduction, mesh cleaning, etc.) can be done in MeshLab.