Meshes

Deborah Schmidt

Head of Helmholtz Imaging Support Unit, MDC Berlin

Sep 17, 2025

Slides available at https://ida-mdc.github.io/workshop-visualization/2-1_in-depth-meshes/

Converting voxel datasets into meshes

Fixed thresholds: Used to generate meshes by separating foreground from background using a set intensity threshold.
Content-based annotations: Create precise meshes by using annotated regions to define boundaries.
Machine learning & interactive labeling: Interactive tools combine user input with AI predictions to refine boundaries.

© Müller et al. https://doi.org/10.1083/jcb.202010039

Converting voxel datasets into meshes

Marching Cubes

Marching cubes algorithm. Credit: Ryoshoru, Jmtrivial on Wikimedia, CC BY-SA 4.0

Converting volumetric datasets into meshes

Conversion scripts

Install and activate environment (guide)
Download Notebook voxel_rendering_napari.ipynb into workshop directory
Type jupyter lab and press Enter
Open Notebook from list of files on the left side
Run Cells in the Notebooks one by one by pressing Shift and Enter

Mesh processing

Reducing mesh complexity

Decimation: A process to reduce the number of polygons in a mesh while maintaining the overall shape and detail.
Remeshing: Tools like MeshLab and Blender offer remeshing techniques that can optimize mesh topology for better performance.
LOD (Level of Detail): Use LOD techniques to switch between different levels of mesh complexity based on the viewer’s distance.

Rendering meshes

Rendering meshes with Blender

Separate tutorial - click this box!

Rendering in Blender

In this section, we will cover specific Blender features to help you create beautiful renderings from scientific datasets. Blender is a powerful tool for this purpose, but it has a steep learning curve, so we’ll break it down step-by-step.