Open-Source 3D Imaging Platforms for CBCT and Maxillofacial Research

This page is for dental researchers, postgraduate students, teachers and the IT people who support them: anyone who needs to do more with a CBCT scan than scroll through it. Segmenting a mandible, rendering a skull for a lecture, superimposing two scans taken years apart or exporting an STL for a 3D printer all need a 3D imaging platform, and several good ones are free and open source.

The short answer: for CBCT segmentation and STL export, start with MITK, which is actively developed and has AI-assisted segmentation. For craniofacial measurements and scan superimposition, use 3D Slicer with SlicerCMF. For publication-quality rendering, Voreen. Be clear about one thing from the start: none of these is a dental implant planner or surgical guide designer, and none is cleared for clinical use. They are research and teaching tools.

The short list

Research use only: what that means in practice

Every tool here says, in one way or another, that it is not a medical device. 3D Slicer’s licence states it is designed for research purposes only and has not been reviewed or approved by the FDA. CustusX’s developers say it is neither FDA nor CE approved, not intended for routine clinical use, and that patient use belongs only inside a clinical study with anonymised data. MITK and Voreen present themselves as research software. For a practice, the consequence is simple: use these platforms for studies, teaching, case presentations and 3D-printed demonstration models, not for diagnosis or treatment decisions. Anonymise scans before they leave the clinic, especially if they go to a university workstation or a GPU server.

MITK (Medical Imaging Interaction Toolkit)

MITK from the German Cancer Research Center (DKFZ) is the most practical all-rounder for CBCT work. Its DICOM Browser scans a disc copy, and the Segmentation view offers manual tools with interpolation, 3D thresholding, Otsu and GrowCut, plus AI-assisted nnInteractive (segment from a few clicks) and TotalSegmentator. “Create smoothed polygon model” turns a segmentation into a surface you save as STL. Release 2026.06 runs on Windows, Apple Silicon and Intel Macs and Ubuntu. Limits: no dental modules, no implant planning or guide design, a steep interface, and AI tools that are slow without a GPU with around 6 GB of video memory. Choose it if you need to segment jaws, teeth or lesions and export models.

SlicerCMF

SlicerCMF is the only tool on this list built for dentistry. It is a bundle of 3D Slicer modules from the DCBIA group (University of Michigan School of Dentistry and UNC Chapel Hill): CMFreg superimposes follow-up CBCT scans on the cranial base, Q3DC computes 3D cephalometric distances and angles and exports them to CSV, and ModelToModelDistance with ShapePopulationViewer shows colour-coded surface changes. Install it from the 3D Slicer Extension Manager; the old standalone packages are unmaintained. The bundle’s code has not changed since April 2022, though it still builds for 3D Slicer 5.12.4. For maintained work inside 3D Slicer, the same group’s Automated Dental Tools and the DentalSegmentator extension add automatic CBCT segmentation. Pick it for orthodontic, TMJ and orthognathic outcome research.

Voreen

Voreen (Volume Rendering Engine) from the University of Münster is about how a volume looks. VoreenVE builds pipelines by connecting processors in a visual network editor, with direct volume rendering, isosurfaces, 2D transfer functions, clipping planes, ambient occlusion and video export. For dentistry that means clean renderings of a CBCT with bone opaque and soft tissue faded out, for papers and lectures. It also has basic segmentation (random walker, thresholding) and isosurface extraction. Limits: no macOS package, a real learning curve, no dental tools, and no new binary since January 2025, although development continues in the public repository. Choose it when rendering quality matters more than segmentation.

AMIDE

AMIDE is a compact GPL tool for volumetric analysis. Its strengths are fused views of two data sets, rigid registration with fiducial markers and 3D regions of interest (ellipsoids, cylinders, boxes, isocontours) with statistics, plus volume rendering and fly-through movies. In a dental study you can align a baseline and a follow-up CBCT on stable landmarks and compare them slice by slice. Two cautions: CBCT grey values are not calibrated Hounsfield units, so treat densities as relative, and AMIDE has no segmentation-to-STL workflow. Version 1.0.7 (July 2026) revived development but is source-only; Windows users get 1.0.6 installers from 2022. Choose it for registration and ROI statistics.

CustusX

CustusX from SINTEF in Norway is a navigation research platform: it combines preoperative CT or MRI with tracked instruments, video and intraoperative ultrasound. For dental researchers it can import a CBCT, threshold bone, run the Contour filter and export an STL, and on a skull or jaw phantom it can demonstrate landmark registration with a tracked pointer. It has no implant, nerve or guide workflow; its published uses are in neurosurgery, laparoscopy, bronchoscopy and similar fields. Ubuntu is the best-tested platform; a Windows installer is new since v26.08, and there is no Mac version. Consider it only if your project is about navigation or tracking hardware.

3DimViewer

3DimViewer is the simplest route from CBCT to STL: load the series, set a density threshold that captures bone and teeth, create the surface model, export. It also offers three-plane views, GPU volume rendering and support for Planmeca multi-frame dental CT added in version 1.4. It is dormant, though: the last official installers are 3.1.1 from January 2017, officially for Windows Vista to 8 and a pre-Apple Silicon macOS. Threshold models pick up noise and metal scatter, so expect cleanup. Use it for a quick teaching model on a machine where it still runs; for new projects, MITK does the same job with current support.

Open Anatomy Project

The Open Anatomy Project from the Surgical Planning Laboratory at Brigham and Women’s Hospital is a reference, not a processing tool. Its web atlases pair labelled 3D models with the source CT or MRI slices, and bookmarks and shared sessions work well in a seminar. There is no dental atlas: the closest is the SPL Head and Neck Atlas, with the skull, mandible, muscles, vessels and glands, but no teeth listed as separate structures. It runs in a desktop browser only. Use it for head and neck orientation in teaching; for tooth-level models, segment your own anonymised CBCT in MITK or 3D Slicer.

From CBCT to STL: the common workflow

1. Export the CBCT as DICOM and anonymise it.
2. Load it in MITK (DICOM Browser), 3D Slicer or 3DimViewer and check orientation in all three planes.
3. Segment: start with a threshold for bone, then refine by hand or with AI tools. Set the threshold per scan, because CBCT grey values differ between machines.
4. Remove scatter around metal restorations and separate structures you do not need.
5. Create a smoothed surface model and save it as STL.
6. Close holes and trim the mesh in a mesh editor such as Autodesk Meshmixer, which is free but discontinued (final version 3.5), before printing.

How to choose

1. Define the output: a model (MITK, 3DimViewer), a measurement table (SlicerCMF), a figure or video (Voreen), a registration or ROI statistic (AMIDE), or a navigation experiment (CustusX).
2. Check the platform: Voreen and CustusX have no Mac packages; MITK and 3D Slicer run on Windows, macOS and Linux.
3. Check the hardware: AI segmentation in MITK and rendering in Voreen want a capable GPU.
4. Prefer maintained tools for anything you will repeat or publish; treat 3DimViewer and the SlicerCMF bundle as legacy.
5. If you only need to open and look at a scan, a viewer is enough; see our free DICOM viewers for dental CBCT hub.

FAQ

What is MITK used for?

MITK is a free, open-source workbench for viewing, segmenting, measuring and registering medical images. In dental research it is used to segment CBCT scans and export STL surfaces.

What is the best free CBCT segmentation software?

MITK, for its manual and AI-assisted tools and current releases. Inside 3D Slicer, the Automated Dental Tools and DentalSegmentator extensions add automatic dental CBCT segmentation. 3DimViewer is simpler but no longer developed.

Can I plan dental implants with open-source 3D imaging software?

No. None of the platforms here includes implant libraries, nerve tracing or guide design, and none is approved for clinical use.

Is 3D Slicer good for dental CBCT research?

Yes. It is free, runs on Windows, macOS and Linux, and its extensions, including SlicerCMF, cover superimposition, 3D cephalometrics and surface distance analysis. Its licence limits it to research use.

How can I export an STL from a CBCT scan for free?

Segment the bone or teeth in MITK or 3DimViewer, create a surface model and save it as STL, then clean the mesh before printing.

Which of these tools run on a Mac?

MITK (macOS 13 or later), 3D Slicer with SlicerCMF, and the Open Anatomy atlases in a browser. 3DimViewer has an old 2017 Mac build; Voreen and CustusX have no Mac packages.

Last updated: 28 September 2026 · DentSoftPro editorial team. Licence, version and platform details are checked against each developer's official documentation; none of the tools listed here should be treated as a certified medical device unless its vendor says so.