Interactive Three‐Dimensional Stromatolite Visualisation

Interactive render of the emergent three-dimensional domed stromatolite surface produced by the circular domed growth model

The interactive visualisation provides a three-dimensional representation of the stromatolite surface generated by the growth model.

Rather than displaying only the final morphology, the visualisation can browse through the representative growth layers generated during the simulation, allowing the evolution of the stromatolite surface to be explored interactively.

Unlike the numerical models, the visualisation performs no biological or ecological simulation. Instead, it reads the processed layer surface output generated by the 3D growth models and converts it into a standalone interactive HTML document that can be explored in any modern web browser.

The resulting visualisation allows the stromatolite surface to be rotated, zoomed, inspected and replayed through time, making it easier both to appreciate the final morphology and to understand how it emerged.

Unlike the numerical models, the visualisation performs no biological or ecological simulation. Instead, it reads the output generated by the 3D growth models and converts it into an interactive HTML document that can be explored in any modern web browser.

Rendering Pipeline

3D Rendering Pipeline

Worked Example - the 3D Circular Domed Model

1. Run the 3d_circular_domed_model.ipynb notebook
2. This creates the stratigraphy file data/output/3d-circular-domed-stratigraphy.npz
3. With the project virtual environment activated, run the layer surface builder:

python src/build-layer-surfaces.py --input data/output/3d-circular-domed-stratigraphy.npz --output data/output/3d-circular-domed-layer-surfaces.npz

4. With the project virtual environment activated, run the interactive 3D render generator on the layer surfaces file generated by step 3:

python src/render-interactive-dome.py --dark-mode --input data/output/3d-circular-domed-layer-surfaces.npz

5. This creates an interactive HTML render with the same path and name as the layer surfaces file but with a "html" extension:

data/output/3d-circular-domed-layer-surfaces.html

6. Open the HTML file in a web browser to view the render

Interactive Controls

The generated HTML visualisation provides several interactive controls.

• Rotate, pan and zoom the stromatolite surface.
• Browse between representative growth layers using the layer slider.
• Replay the stored growth history using the Play and Pause controls.
• Inspect the stromatolite from any viewing angle.

These controls allow both the final morphology and the development of that morphology through time to be explored directly within the browser.

Relationship to the Growth Model

The interactive visualisation is a presentation layer rather than an extension of the stromatolite growth model.

All biological growth, ecological forcing and geometric development are completed before the rendering stage begins. The renderer performs no numerical simulation, introduces no additional biological processes and does not modify the model output in any way.

Instead, it simply converts the final simulated stromatolite surface into an interactive three-dimensional visualisation that can be explored from any viewpoint.

The scientific results are therefore produced entirely by the growth model itself. The interactive renderer introduces no additional modelling or interpretation. Its purpose is to communicate and explore the simulated results, allowing both the final stromatolite morphology and its development through time to be examined interactively.