Version 1.5.0

Interactive Growth Visualisation

This release introduces an interactive three-dimensional visualisation pipeline for exploring simulated stromatolite morphology.

The renderer has been redesigned to work from representative growth layers extracted from the model stratigraphy, allowing the development of the stromatolite surface to be explored interactively while remaining completely separate from the underlying biological simulation.

Added

• New layer surface generation pipeline producing compact browser-ready surface datasets from full stratigraphy files
• Interactive HTML renderer supporting all 3D growth models
• Layer slider for browsing representative growth stages
• Play/Pause controls for replaying stromatolite development through time
• Improved rendering of local surface morphology by using representative layer surfaces directly
• Standalone Plotly HTML output requiring no Python environment to view

Improved

• Rendering workflow separated into three distinct stages:
  1. Biological growth simulation
  2. Representative layer extraction
  3. Interactive visualisation
• Documentation expanded to describe the rendering pipeline and interactive exploration workflow
• Workflow diagrams updated to illustrate the complete visualisation pipeline

Scientific Notes

This release does not alter the biological growth model.

The interactive renderer performs no numerical simulation and introduces no additional biological processes. It simply presents the model output in an interactive form, making both the final stromatolite morphology and its development through representative growth layers easier to explore and communicate.

Version 1.4.0

Refactoring

• Read all geometric properties from configuration files rather than hard-coding
• Refactor the data folder structure so configuration files and output are separated
• Move common code to a common Jupyter Notebook

Version 1.3.0

Three-Dimensional Circular Stromatolite Model

This release introduces a three-dimensional circular masked stromatolite model, extending the existing 3D framework to produce a circular microbial colony more representative of natural stromatolites.

The underlying biological model remains unchanged. Instead, this release demonstrates how a substantial increase in morphological realism can be achieved simply by changing the geometry of the growth domain while preserving the same governing equations for microbial growth, sediment accumulation, burial and environmental forcing.

Added

• Three-dimensional circular masked stromatolite implementation
• Circular growth domain centred within the computational grid
• Masked surface rendering and diagnostics
• Circular surface snapshots and final 3D visualisations
• Cross-sectional extraction through the completed circular colony
• Updated documentation describing the new implementation and its interpretation

Improved

• Extended the progression of spatial models from:
  • One-dimensional reference model
  • Two-dimensional cross-section
  • Three-dimensional rectangular surface
  • Three-dimensional circular colony
• Expanded Wiki documentation to reflect the new implementation and its role within the overall modelling framework
• Updated project documentation to reflect the transition from computational framework development towards investigations of stromatolite morphology

Notes

This release represents an important milestone in the project.

Previous versions progressively extended the biological model from one to three spatial dimensions. Version 1.3.0 demonstrates that simply changing the spatial geometry—from a rectangular computational domain to a circular microbial colony—produces a morphology immediately recognisable as a stromatolite without introducing additional biological complexity.

As with previous releases, the emphasis remains on allowing increasingly realistic morphology to emerge from simple ecological interactions rather than prescribing it directly.

Version 1.1.0

Two-Dimensional Cross-Section Model

This release extends the project from a single one-dimensional growth column to a two-dimensional cross-sectional model, representing the first step towards modelling stromatolite morphology rather than simply vertical growth through time.

Added

• Two-dimensional cross-sectional growth model.
• Independent vertical growth columns distributed across a horizontal substrate.
• Cross-sectional visualisation of stromatolite development through time.
• Time-series animation of evolving morphology.
• Additional diagnostic plots for interpreting spatial growth behaviour.
• Comprehensive project documentation and Wiki pages describing the new model and its outputs.

Model

The two-dimensional implementation treats each horizontal position as an independent one-dimensional growth model experiencing the same environmental forcing. Although neighbouring columns do not yet interact mechanically or biologically, their differing growth histories produce realistic large-scale stromatolite cross-sectional forms.

This architecture provides a direct extension of the validated one-dimensional model while establishing the framework for future spatial interactions.

Documentation

The accompanying Wiki has been expanded with:

• Two-Dimensional Cross-Section Model
• Interpreting the Two-Dimensional Model
• Updated Home page
• Revised descriptions of the core growth model and supporting processes

Looking Ahead

This release establishes the spatial framework needed for future developments, including:

• Lateral interactions between neighbouring microbial mats.
• Sediment redistribution across the surface.
• Fully three-dimensional stromatolite growth.
• More realistic domed geometries.

As with previous releases, the emphasis remains on building incrementally: extending the model while preserving clarity and physical interpretability.

Version 1.0.0

Initial public release

This release marks the first public version of the Stromatolite Growth Modelling project.

The project explores the emergence of stromatolite-like structures through the interaction of microbial growth, sediment deposition and environmental processes. Rather than reproducing a specific fossil, the model provides a computational framework for investigating how layered structures can arise from relatively simple biological and environmental rules.

Features

• Biological growth model
• Sediment deposition and burial
• Layer-by-layer stromatolite development
• Environmental forcing
• Seasonal light cycle
• Annual temperature variation
• Variable sediment supply
• Stochastic burial events
• Water-depth-dependent light attenuation
• Animated model outputs
• Configurable model parameters for experimentation

Repository

This initial release includes:

• Source code
• Example notebooks
• Project documentation
• Example outputs
• GitHub Wiki (under development)

Looking Ahead

Future development is expected to explore more sophisticated environmental interactions, additional biological processes, higher-dimensional growth models and comparisons with fossil morphologies as the project evolves.

This release establishes the core modelling framework on which future development will build.