Written and maintained by CASRAI Editorial Board
Last updated
3D Slicer is a free, open-source desktop application for visualizing and analyzing medical image data, used by researchers and by teams building imaging products. It is not the same thing as a 3D-printing slicer such as UltiMaker Cura or PrusaSlicer, and it is not approved for clinical use. This guide is for researchers and lab staff who need to know what 3D Slicer does, which file formats it opens, and what a basic session looks like. It is general software information, not medical advice.
What 3D Slicer is
According to its official user guide, 3D Slicer is “a software application for visualization and analysis of medical image computing data sets.” It serves as a research platform and as a platform for product development. It runs on Linux, macOS and Windows, and it can display data on the desktop and in virtual reality. It works with images, segmentations, surfaces, annotations and transformations, in 2D, 3D and 4D.
3D Slicer versus 3D-printing slicers
The name causes a common mix-up. Searches for “3D slicer” also return print-preparation tools, and related searches such as “3D slicer Cura” show the overlap. The two groups of software do different jobs.
| Software | What it is | Typical input |
|---|---|---|
| 3D Slicer (slicer.org) | Medical image computing platform for visualization and analysis | DICOM, NRRD, NIfTI and other imaging files, plus surface models |
| UltiMaker Cura | 3D-printing and slicing software, as titled on its own site | 3D models for printing |
| PrusaSlicer | Slicer for 3D printing, published by Prusa | 3D models for printing |
The only direct link in the official documentation is that 3D Slicer can load surface models in STL, OBJ, PLY and VTK formats, the same kinds of model files that print software works with. This guide covers the medical imaging platform only.
Who runs it and what it covers
3D Slicer is distributed under a BSD-style open-source license. The user guide says the license places no restrictions on legal uses, and that the project avoids code under GPL or other copyleft terms because of medical-specific provisions. The National Institutes of Health is described as a major contributor through competitive grants and contracts. The guide does not state a funding total, so none is given here.
Functions are split into modules, and extensions add further modules. The Extensions Manager lets you browse, install and uninstall extensions. Core modules named in the getting-started guide include Volumes, Segment Editor, Markups and Transforms. Radiotherapy and ultrasound DICOM data load through extensions rather than the base application.
Which file formats 3D Slicer opens
The data loading page of the user guide lists the formats below.
| Data type | Formats and notes |
|---|---|
| Images (clinical) | DICOM: CT, MRI, PET, X-ray, some ultrasound, SEG and parametric maps; RT and ultrasound objects need extensions |
| Images (research) | NRRD (.nrrd, .nhdr); MetaImage (.mha, .mhd); NIfTI-1 (.nii, .nii.gz); VTK (.vtk, which carries no axis directions) |
| Not loadable or discouraged | NIfTI-2 cannot be loaded; the Analyze format is discouraged |
| Other image formats | TIFF, PNG, JPEG, BMP, GIPL, MGZ, MRC, Scanco ISQ, BioRad PIC; RAW and MVL need the RawImageGuess extension |
| Models | VTK, VTP, VTU, STL, OBJ, PLY |
| Segmentations | .seg.nrrd, labelmap NRRD or NIfTI, closed-surface .vtm |
| Scenes | .mrml, or the .mrb bundle |
| Markups | .mrk.json is recommended; .fcsv is deprecated |
If a format fails to load, the documentation points users to the Slicer forum to report it.
How a basic session works
The documented workflow is load, view, process, save. The steps below follow the official getting-started and data loading pages.
- Start Slicer and use the Welcome panel to load your own data or sample data.
- To load files, drag and drop them into the window or choose File > Add Data.
- For DICOM, add the files to the DICOM database through the DICOM module or toolbar button, then double-click the items in the DICOM browser to load them.
- Open the Data module and its Subject hierarchy tab to see what is in the scene. The eye icon toggles an item’s visibility.
- Use the slice viewer bar to scroll through slices.
- Process data with modules such as Volumes, Segment Editor, Markups or Transforms.
- Save work with File > Save data.
Many research projects share image data across tools. Choosing open formats such as NRRD or NIfTI-1, and keeping a record of the software version used, supports the reuse goals described in the FAIR data principles.
Strengths and limits
- Open license. The BSD-style license is open-source and permits any legal use.
- Extensible. Extensions add capabilities, so the base install stays focused.
- Cross-platform. It runs on Linux, macOS and Windows.
- Not approved for clinical use. The official guide states plainly that Slicer is not approved for clinical use. It is intended for research, and the user is responsible for any permissions and compliance that apply.
- Format limits. NIfTI-2 files do not load, and RAW files need an extension.
Software used in research can itself be a citable output. See open-source software and the FAIR4RS and software citation principles for how to credit it. For other open-source image-analysis tools aimed at specific fields, see the CASRAI guides to QuPath (digital pathology) and CellProfiler (cell images).
FAQ
Is 3D Slicer free?
Yes. It is distributed under a BSD-style open-source license with no restrictions on legal uses, according to the official user guide.
Is 3D Slicer for 3D printing?
No. It is a medical image computing platform. It can load model files such as STL and OBJ, but it does not replace print slicers like Cura or PrusaSlicer.
Can 3D Slicer be used for clinical care?
No. The official documentation states that Slicer is not approved for clinical use and is intended for research. Users are responsible for permissions and compliance.
Which operating systems does it support?
Linux, macOS and Windows.
Sources
- About 3D Slicer, Slicer user guide, read 2026-11-07.
- Getting Started, Slicer user guide, read 2026-11-07.
- Data Loading and Saving, Slicer user guide, read 2026-11-07.
