3D Slicer: Export Models and Share Them as Interactive 3D

3D Slicer is one of the most widely used free tools for segmenting CT and MRI data. Getting a segmentation out of Slicer and in front of reviewers, students, or colleagues is a separate problem. This guide covers the export options and how to turn the result into a 3D link anyone can open.

Two routes out of Slicer

There are two good ways to move a Slicer segmentation to a shareable viewer:

1. Export surface models (STL or OBJ). Slicer builds the 3D surfaces and you upload the meshes.
2. Save the segmentation itself (.seg.nrrd). You upload the label map and the surfaces are built on upload, one layer per segment.

Route 2 is usually better for multi-structure segmentations, because segment names and colours travel with the file. Route 1 is useful when you have already smoothed, decimated, or edited the surfaces in Slicer.

Route 1: export STL or OBJ from Slicer

1. Open the Segmentations module and select your segmentation.
2. Expand Export/import models and labelmaps.
3. Choose Export to files, pick the output folder, and set the format to STL or OBJ.
4. Tick Merge into single file if you want one file for all segments. Leave it unticked for one file per segment.
5. Check the size scale and coordinate system settings. Slicer works in millimetres, so keep that unit in mind for the next step.

Then upload the file to AcademicAR and set the source unit to millimetres. A single STL becomes one mesh. If readers should toggle structures separately, prefer OBJ or the .seg.nrrd route below.

Route 2: save the segmentation as .seg.nrrd

1. In Slicer, use File → Save (or Save Data).
2. Make sure the segmentation node is ticked and saved as .seg.nrrd.
3. Upload that file to AcademicAR as a medical segmentation.

On upload, each non-empty segment becomes its own named, coloured layer, with up to 64 layers per model. NIfTI (.nii/.nii.gz), DICOM-SEG, and a ZIP of masks work the same way if your pipeline produces those instead (see our post on segmentation formats).

Medical uploads need an extra confirmation that the data is anonymised and that you have the right to share it. The raw file is deleted after conversion.

What your readers get

The result is a viewer link and a QR code. Readers can:

• show, hide, fade, or recolour each structure in the Layers panel,
• cut through the model with the section plane and read the cut in the colour-coded slice view,
• see structure dimensions and distances between layers where layer measurements are enabled,
• open the model in AR on iPhone or Android at its real size.

You can also save a default layer view and scenes that walk readers through the anatomy step by step.

Starting from the DICOM instead

If you haven’t segmented yet and only need bone or skin surfaces, you can skip Slicer and upload the DICOM series as a ZIP with a threshold preset or a custom Hounsfield range. See From DICOM to Interactive 3D and Hounsfield units explained.

Before you publish

• Remove faces and identifying features from head and neck reconstructions.
• Confirm consent and ethics approval cover publication of the 3D data.
• Name your segments clearly in Slicer: those names become the legend your readers see.

Create a free account and share your first Slicer segmentation as an interactive 3D model.