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Volumetric Dataset Rendering in Python

Deborah Schmidt
Helmholtz Imaging | MDC Berlin
Sep 25, 2024
Slides available at https://ida-mdc.github.io/workshop-visualization/tutorial-volume-rendering-python/

Volume Rendering in napari

  • Interactive visualization and annotation: Offers tools for exploring data and annotating images in real-time.
  • Layer-based rendering: Supports multiple layers like images, labels, points, and shapes for versatile data representation.
  • Plugin extensibility: Easily extendable through plugins to add custom functionality.
  • Integration with Python ecosystem: Seamlessly works with NumPy, Dask, and other scientific Python libraries.

Volume Rendering in napari

Solution to run napari code through Album

To simplify and unify solutions used in our tutorials, we use Album, a tool for capturing and sharing specific software use cases in dedicated virtual environments.

Click the solution box next to this text and follow the displayed usage instructions to run the solution either from command line or graphical interface.

Launch napari v0.5.3

visualization:launch-napari:0.2.0

This solution launches napari with the option to directly open a dataset.
Tags: template, napari

Volume Rendering in napari

Dependencies

Link to full source code

58    dependencies={'environment_file': """channels:
59  - conda-forge
60dependencies:
61  - python=3.11
62  - scikit-image=0.24.0
63  - pyqt=5.15.9
64  - pip
65  - pip:
66    - napari==0.5.3
67"""}

Volume Rendering in napari

Running napari programmatically

Link to full source code

 8    import napari
 9    from skimage.io import imread
10    from album.runner.api import get_args
11
12    # Get input parameters
13    input = get_args().input
14    is_rgb = get_args().rgb
15
16    if input:
17        # Show provided image
18        img = imread(input)
19        napari.view_image(img, rgb=is_rgb, name="Input image")
20    else:
21        # Launch empty viewer
22        napari.Viewer()
23
24    napari.run()

Volume Rendering with Pygfx

Key Features:

  • Real-time GPU Rendering: Leverages modern GPU acceleration for high-performance 2D and 3D graphics.
  • Diverse application support: from scientific visualization to video game rendering.
  • Flexible Scene Graph: Employs a scene graph architecture to efficiently manage complex scenes.
  • Custom Shader Support: Allows for custom shaders to create advanced visual effects.

Volume Rendering with Pygfx

Solution to run pygfx code through Album

To simplify and unify solutions used in our tutorials, we use Album, a tool for capturing and sharing specific software use cases in dedicated virtual environments.

Click the solution box next to this text and follow the displayed usage instructions to run the solution either from command line or graphical interface.

Render a volume using Pygfx

visualization:render-volume-pygfx:0.1.0

In this solution, volumes can either be rendered as isosurface or using raycasting.

Volume Rendering with Pygfx

Dependencies

Link to full source code

88    dependencies={'environment_file': """channels:
89  - conda-forge
90dependencies:
91  - python=3.11
92  - pygfx=0.5
93  - pyside6=6.7
94  - imageio=2.35
95"""}

Volume Rendering with Pygfx

Setting the scene

Link to full source code

18    # Set up the canvas and scene
19    canvas = WgpuCanvas()
20    renderer = gfx.renderers.WgpuRenderer(canvas)
21    scene = gfx.Scene()

Volume Rendering with Pygfx

Adding the volume to the scene

Link to full source code

23    # Read the input dataset
24    voldata = iio.imread(image_path).astype(np.float32)
25
26    # Set the volume rendering type
27    if isosurface:
28        # Render volume as isosurface
29        geometry = gfx.Geometry(grid=voldata)
30        material = gfx.VolumeIsoMaterial(clim=(0, 2000), threshold=1000)
31        vol = gfx.Volume(geometry, material)
32    else:
33        # Render volume using raycasting
34        tex = gfx.Texture(voldata, dim=3)
35        vol = gfx.Volume(
36            gfx.Geometry(grid=tex),
37            gfx.VolumeRayMaterial(clim=(0, 2000), map=gfx.cm.cividis, pick_write=True),
38        )
39
40    # Add the volume to the scene
41    scene.add(vol)

Volume Rendering with Pygfx

Setting up the camera and running the application

Link to full source code

40    # Add the volume to the scene
41    scene.add(vol)
42
43    # Set up the camera to show the scene
44    camera = gfx.PerspectiveCamera(70, 16 / 9)
45    camera.show_object(scene, view_dir=(-1, -1, -1), up=(0, 0, 1))
46
47    # Enable interactive rendering
48    controller = gfx.OrbitController(camera, register_events=renderer)
49
50    def animate():
51        renderer.render(scene, camera)
52        canvas.request_draw()
53
54    canvas.request_draw(animate)
55    run()

Volume Rendering in VTK

  • Transfer Functions: Map voxel intensities to color and opacity for flexible and accurate rendering.
  • Advanced customization: Full control over lighting, shading, and rendering parameters.
  • ParaView & 3D Slicer: GUI-based tools built on VTK for easier interaction with volumetric data.
Separate tutorial - click this box!

Rendering meshes in VTK

Learn how to render 3D meshes in VTK and get insights into the Python code behind it.
2024 | HELMHOLTZ IMAGINGExit slides