Visualization, segmentation, quantification, registration and 3D model export in 3D Slicer using real world MicroCT data

What you'll learn
- Confidently use 3D Slicer to visualize and explore CT and Micro-CT data in 2D and 3D
- Correctly load CT datasets, image stacks, and NRRD files while managing voxel size and resolution
- Create high-quality segmentations using thresholding, smoothing, islands, logical operators, and advanced tools
- Separate individual objects within a segmentation and analyze them as independent entities
- Perform accurate measurements using markups (distances, angles, areas) and export results for further analysis
- Run quantitative analysis using Segment Statistics (volume, surface area, porosity, defect size distribution)
- Segment complex structures where pores and surrounding air have similar intensities
- Calculate porosity from CT and Micro-CT data using robust, reproducible workflows
- Install and use essential 3D Slicer extensions to extend segmentation and analysis capabilities
- Register multiple CT datasets and align scans acquired at different times
- Register multiple CT datasets and align scans acquired at different times
- Export segmentations as 3D models, meshes, and label maps for visualization or downstream use
- Apply the same workflows to both medical and non-medical CT imaging projects without requiring medical knowledge

Requirements
- No prior experience with 3D Slicer is required.
- No medical or anatomical knowledge is needed.
- Basic computer skills (installing software, managing files and folders)
- Interest in X-Ray CT, Micro-CT, medical imaging, or 3D image analysis.

Description
Learn how to turn X-Ray CT and micro-CT scans into clear visualizations, accurate segmentations, and quantitative results and 3D models using3D 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 Sliceris 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 bothnon-medicalandmedical imagingprojects.

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 includedso 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.

By the end of this course, you will be able to

Confidently use 3D Slicer for CT and Micro-CT image analysis

Design and execute complete segmentation and analysis workflows

Quantify volumes, surfaces, porosity, and structural changes

Export results and models for reporting, further analysis, or visualization

Apply the same concepts to any CT dataset — medical or non-medical

I am an X-ray microscopy (XRM) and Micro-CT application scientist with more than a decade of experience working with CT data across industry, research, and academia.

I've trained users in fields ranging from pharmaceuticals and energy storage to additive manufacturing, oil & gas, and medical imaging — and this course is built exactly the way I teach in real projects:clear explanations, real data, and workflows that actually work.

Who this course is for:
- Beginners who want to learn 3D Slicer from scratch with no prior experience.
- Medical imaging professionals (radiology, dentistry, research, biomedical engineering) who want a practical, workflow-based introduction to 3D Slicer.
- Researchers and engineers working with CT or micro-CT data in materials science, additive manufacturing, energy storage, oil & gas, geoscience, or pharmaceuticals.
- Students and academics looking to understand segmentation, measurement, registration, and quantitative analysis in real CT datasets.
- 3D printing and modeling enthusiasts who want to extract accurate 3D models from CT or micro-CT scans.
- Industry professionals who need reliable, repeatable workflows for CT-based inspection, defect analysis, and porosity measurement.
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