3D Data Visualization Workshop @ HIDA, September 2026
Sep 24, 2026
Workshop 3D Data Rendering
With the Helmholtz Imaging Support Unit @ MDC Berlin
Monday
- 12pm Installation time
- 1pm Lunch
- 2pm Introduction, general remarks, overview of 3D Data rendering
- 2:45pm Image Quality Control (Pixel Patrol)
- 3:45pm Coffee
- 4:15pm Volumetric Data Rendering
- Overview Slides
- Notebook: voxel_rendering_napari.ipynb - the same viewer, driven from Python (requirements)
- Notebook: voxel_rendering_vtk.ipynb - transfer functions by hand (requirements)
- Notebook: voxel_rendering_pygfx.ipynb - the same volume on the GPU through wgpu (requirements)
- Large 3D data
- Notebook: tiff_to_ngff_and_neuroglancer.ipynb - TIFF to OME-Zarr, and into Neuroglancer (requirements)
- Notebook: luxar_gaussian_splats.ipynb - needs an NVIDIA GPU (requirements)
- Overview Slides
Tuesday
- 10am Meshes
- Meshes and converting voxels to meshes
- Notebook: voxel_to_mesh.ipynb - the conversion
- Notebook: mesh_rendering_tutorial.ipynb - rendering meshes from a script
- Basic mesh rendering in Blender
- Mesh cutting in Blender
- Ways to make things transparent in Blender
- 11:00am Blender & Microscopy Nodes demo
- 12:00am Getting To Know Your Data with Jochen Müller (Stiftung Planetarium Berlin)
- 1pm Lunch
- 2pm Colors
- 2:15pm Point Clouds Demo
- Slides
- Notebook: point_clouds_tutorial.ipynb - visualize by color, by property, and by normal
- Point clouds in Blender
- 2:30pm Vector Fields
- Slides: Google or Here
- Notebook: vector_field_visualization.ipynb - the figures behind those slides (requirements)
- 3pm Open Working Time
Wednesday
- 9am Open Working Time
- 1:30pm Lunch
- 3pm Encounters in the Milkyway, Zeiss Planetarium Berlin
Thursday
- 10am VR Showcase
- 10:30am Open Working Time
- 1pm Lunch
- 3pm Presentation & Feedback
- 5pm End of workshop