How to Leverage 3D Slicer for Medical Imaging Research & Product Development

April 29, 2025

Sam Horvath, Jean-Christophe Fillion-Robin and Andinet Enquobahrie

AutoscoperM Hierarchical 3D Registration in Action: AutoscoperM’s Hierarchical 3D Registration extension for 3D Slicer automates six-DOF rigid alignment of skeletal anatomy. In this example, tracking a metacarpal bone across a 3D CT sequence. It defines ROIs around each bone, registers the root node first, then propagates optimized transforms through the anatomical hierarchy for accurate motion and kinematic analysis.

If you’re working at the intersection of medical imaging research and product development, chances are you’ve heard of 3D Slicer—the free, open source software platform transforming how we visualize, analyze, and process medical images. But knowing what’s possible with 3D Slicer is only half the battle. The real question is: how can you tailor it to meet your unique needs?

In our recent webinar, we explored how Kitware’s expertise in 3D Slicer can help you do just that—whether you’re building a new application, enhancing your research, or developing commercial products.

If you have time, we recommend watching the full webinar recording to see real-world examples and a live demo. Otherwise, keep reading for the highlights and key takeaways!

Why More Medical Teams Are Turning to 3D Slicer

3D Slicer is more than just a visualization tool—it’s a full-featured, open source platform designed to drive innovation in medical image computing. With no licensing fees and a permissive BSD-style license, 3D Slicer removes traditional barriers to adoption, making it ideal for both research institutions and product developers.

Capable of adapting to your workflow, 3D Slicer supports your unique clinical and product development needs due to its breadth of functionality across clinical and translational workflows. The platform enables seamless DICOM standard interoperability, supporting a wide array of medical image formats, structured reports, and radiation therapy data, making it easier to integrate with hospital systems and imaging devices.

Its modular architecture supports advanced capabilities like:

AI-powered segmentation and analysis
Image registration and procedural guidance
Cloud-based deployment and browser access
VR/AR support
Python scripting and extensibility

TotalSegmentator Extension in Action: An AI-powered 3D Slicer extension that delivers fully automatic, whole-body CT segmentation. It leverages the TotalSegmentator model to instantly delineate organs, vessels, and tissues across an entire scan for rapid quantitative analysis. — ***TotalSegmentator Extension in Action:*** An AI-powered 3D Slicer extension that delivers fully automatic, whole-body CT segmentation. It leverages the TotalSegmentator model to instantly delineate organs, vessels, and tissues across an entire scan for rapid quantitative analysis.

Built for Your Use Case

In the webinar, we explored three common ways teams are using 3D Slicer:

As a radiology workstation, it delivers high-performance visualization and diagnostic insights across multiple modalities.
As a research platform, it helps teams develop, test, and validate new algorithms and methodologies
As a product development framework, it offers a fast path to prototypes and custom-branded applications.

Regardless of your starting point, 3D Slicer is designed to scale with your goals.

Shape Population Viewer (SPV) in Action: An illustration of Slicer as a research platform: SPV—a dedicated module in the SlicerSALT custom application—automatically ingests a folder of 4D mesh sequences (boundary or skeletal), then offers intuitive playback controls to animate and explore shape evolution over time. This workflow empowers teams to develop, test, and validate advanced morphological analysis algorithms with minimal setup. — ***Shape Population Viewer (SPV) in Action:*** An illustration of Slicer as a research platform: SPV—a dedicated module in the SlicerSALT custom application—automatically ingests a folder of 4D mesh sequences (boundary or skeletal), then offers intuitive playback controls to animate and explore shape evolution over time. This workflow empowers teams to develop, test, and validate advanced morphological analysis algorithms with minimal setup.

Flexible by Design

One of 3D Slicer’s most powerful features is its ability to be customized at different levels of complexity:

Start with Extensions

You can extend Slicer’s functionality by installing modules, ranging from image analysis tools to device-specific plugins, directly through its Extension Manager.

Streamline the User Experience

For more targeted workflows, “Slicelets” and “Guidelets” offer simplified, task-specific interfaces. These are especially useful for clinical or touch-based applications.

Build Your Own Application

If you’re developing a commercial tool, you can use Slicer’s Custom Application Template to create a standalone app with its own branding, UI, and functionality—without reinventing the wheel.

This tiered approach allows you to start small and scale your customization as your project evolves.

Cell Locator Interface: A cross-platform, open-source Slicer-based application co-developed with the Allen Institute for Brain Science and the BICCN. Cell Locator lets users load a 20× microscopy image of a brain slice, generate a matching virtual slice in a segmented, color-coded 3D atlas (mouse, human, or non-human primate), annotate cell soma positions, and automatically push orientation and coordinate metadata back to the Allen Institute’s LIMS—streamlining the Patch-seq pipeline and precise spatial mapping. — ***Cell Locator Interface:*** *A cross-platform, open-source Slicer-based application co-developed with the Allen Institute for Brain Science and the BICCN.* *Cell Locator* lets users load a 20× microscopy image of a brain slice, generate a matching virtual slice in a segmented, color-coded 3D atlas (mouse, human, or non-human primate), annotate cell soma positions, and automatically push orientation and coordinate metadata back to the Allen Institute’s LIMS—streamlining the Patch-seq pipeline and precise spatial mapping.

Ready to Get Started?

We encourage you to download 3D Slicer (for free, of course!) and explore the tool and it’s features. Here are some helpful resources to help you get started:

⬇️ Download Slicer
🙋 Ask questions in the community forum
🎓 Get professional training
🛠️ Use the SlicerCustomAppTemplate to build your own Slicer desktop application
🔎 Discover how Trame brings Slicer capabilities to the web

Kitware’s Role: Helping You Go Further, Faster

While 3D Slicer offers impressive capabilities out of the box, many research teams and product developers turn to Kitware for advanced customization and support. Our experts can help:

Develop tailored extensions for your specific research or product needs.
Integrate new algorithms and machine learning models.
Support regulatory pathways with validated pipelines.
Optimize performance for large datasets or real-time applications.

Explore our success stories

✨ Customer Highlights: See how companies and industry partners are building commercial products with 3D Slicer.
🔬 Research and Development: Explore case studies that demonstrate how Slicer facilitates cutting-edge medical imaging research and product development.

We also maintain strong ties to the Slicer community and help guide the platform’s evolution through contributions, governance, and support services.

Contact our team to explore how we can help you achieve your goals.

Tags:

3D Slicer 3D Slicer Research and Development AI DICOM Medical and Biomedical Systems Medical Computing Medical Device Medical Image Analysis Medical Imaging Medical Visualization segmentation webinar