Learn how to turn X-Ray CT and micro-CT scans into clear visualizations, accurate segmentations, and quantitative results and 3D models using 3D Slicer. This beginner-friendly, project-based course teaches complete image analysis workflows using real life micro-CT datasets — from 3D visualization and segmentation to measurement, porosity analysis, registration, and 3D model export. No medical knowledge is required, yet all techniques are fully applicable to medical imaging.
3D Slicer is one of the most powerful free tools for CT image visualization, segmentation, and quantitative analysis — yet most tutorials focus narrowly on medical imaging and assume prior clinical knowledge. This course is different. In this project-based 3D Slicer Masterclass, you will learn how to go from raw CT and Micro-CT data to meaningful, quantitative results, step by step — with no prior medical or imaging background required.
You will work hands-on with real Micro-CT datasets and learn practical workflows that are directly applicable to both non-medical and medical imaging projects.
You will learn how to use 3D Slicer as a complete image analysis environment, including:
- Visualizing CT and Micro-CT data in 2D and 3D
- Managing voxel size, resolution, and data formats correctly
- Creating accurate segmentations using thresholding, smoothing, islands, and logical operations
- Performing measurements and markups (distances, angles, areas) and exporting results
- Running quantitative analysis using Segment Statistics (volume, surface area, porosity)
- Separating individual objects and analyzing them as independent entities
- Exporting 3D models and meshes (STL/labelmaps) for further use or 3D printing
- Installing and using 3D Slicer extensions to extend functionality
- Registering multiple CT datasets and quantifying differences between scans
You will follow complete workflows using four real Micro-CT case studies:
- Knight figurine (Micro-CT)
Segment the object into multiple parts and export each section as an independent 3D model and mesh. - 3D-printed metal sample (Micro-CT)
Segment internal spherical defects, separate them into individual objects, and calculate volume and surface area distributions. - Rock sample (Micro-CT)
Segment grains and pores, overcome the challenge of air and pores having identical intensities, and calculate porosity correctly. - Tooth before & after treatment (Micro-CT) (demonstration)
Register two scans, compute the material difference, and quantify how much material was added or removed.
Three full datasets are included so you can follow along step by step. The final dataset is shown as a guided demonstration so you can apply the same workflow to your own data.
