Volume rendering
Prerequisites
Before starting this lesson, you should be familiar with:
Learning Objectives
After completing this lesson, learners should be able to:
Understand the concepts and some methodes of 3-D rendering.
Appreciate that 3-D rendering can be challenging for some data.
Perform basic volume rendering using a software tool.
Motivation
Intuitively grasping 3-D shapes requires visualisation of the whole object. This is not possible when just looking at one or several slices of a 3-D data set. Thus is it important about different volume rendering techniques that can create a 3-D appearance of the whole image. This is especially useful for sparse data, where individual 2-D slices only contain a small subset of the relevant information.
Concept map
graph TD
D("3-D image data") --> R("Volume rendering")
R --> A("2-D image with 3-D appearance")
R -->|VR| AA("Two 2-D images (one per eye)")
R ---|has| M("Many methods and settings...")
Figure
Volume rendering software
| Software | Multi-Channel | Time-lapse | Max-Projection | Volume | Iso-Surface | … | … | … | … |
|---|---|---|---|---|---|---|---|---|---|
| Blender | |||||||||
| Drishti | |||||||||
| ImageJ 3Dscript | |||||||||
| ImageJ 3D viewer | N | N | N | Y | Y | ||||
| ImageJ ClearVolume (Upate Site) | Y | Y | Y | N | N | ||||
| ImageJ Volume Viewer | N | N | Y | Y | N | ||||
| Napari |
Activities
- Example data:
- 3-D+t Chromosome congression
- Useful to see in 3-D rendering (as it is very hard to see what is going on in 2-D slices)
- 3-D EM and segmentation
- EM data is difficult to render in 3-D but for the segmentation channel it is very useful
- Note that the segmentation channel does not look good in a max-projection; actual volume rendering is much better.
- 3-D MRI head
- Good to compare various rendering modes
- 3-D Organoid nuclei
- Challenge: Outer nuclei occulde inner nuclei
- 3-D FIB-SEM
- Challenge: Dense signal, background is bright
- 3-D Tissue segmentation label mask
- Challenge: Epithelial tissue occludes inside
- 3-D+t Chromosome congression
- Open a volume viewer.
- Explore different volume rendering modes (as available in your softwares):
- Maximum projection
- Explore different camera positions
- Volume rendering
- Explore various transparency (alpha) mappings.
- Interesting for 3-D FIB-SEM
- Explore various transparency (alpha) mappings.
- Iso-surface rendering
- Explore various surface thresholds
- Explore changing the light position
- Maximum projection
- Save a snapshot.
- Create and save a custom animation, e.g. rotating the image.
Assessment
True or False
- TODO.
Solution
- TODO
Follow-up material
Recommended follow-up modules:
Learn more: