Royal Netherlands Institute for Sea Research

Shifting biodiversity baselines with 3D Visual modelling of ecosystems

Ecologists have been making mathematical models from the 60s and 70s onwards, as soon as computers became sufficiently powerful to provide reasonable computing times. The models dealt with species interactions, food web dynamics, to name just a few topics. Nowadays, with the computing power that is available with the latest technology, we can make models that detail species interactions and ecosystem processes over many square kilometers, providing a detailed 2D picture of how an ecosystem develops.

Since about the year 2000, computers have become sufficiently powerful to depict ecosystems in 3D, recreating natural landscapes for use in movies (for instance in Lord of the Rings) or in computer games. So far, this technique has mostly been applied to the entertainment industry. With Visual Modelling, we want to use 3D computer-graphics to visualize modelled ecosystems, so that model predictions become better understandable to the general audience, and with this can help scientists, managers and policy makers to outline their plans to the laymen.

In this MSc project, you will make a visual model of an ecosystem for use in a context of nature conservation or natural education. Starting with an (existing) spatial model of an ecosystem, you will develop a pipeline to the (free) 3D modelling software Blender. First you will implement the model in the programming language Python, then you will set up a pipeline (again in Python) that translates the model output to a data form that is usable for Blender, adding non-scientific data and human infrastructure (dykes, paths, etc.) when needed. In Blender, the process of importing is similarly automated using Python scripts that sets up the 3D virtual world, allowing the rendering of images, video material or 3D panorama’s. Finally the output needs to be presented in a useful way, for instance by integrating the videos with standard footage to make a youtube movie, or within a 3D panoramic website.

Examples of this can be found on youtube:

Example of a 3D paranoramic website (in development):


As outlined above, an MSc project in Visual Modelling starts with implementing a model in a programming language, either a new model or an existing one. Hence, experience (or a large interest) in modelling is a requirement. Developing the pipeline and implementing the visualization involves again a lot of programming. Hence, an MSc project in Visual Modelling will entail a lot of programming in Python. A minimal duration of the MSc project of (close to) 6 months is required.

Making a 3D visualization is something that is a study on its own. It involves making a 3D object consisting of a mesh, on which a texture is placed to create a surface that looks like something. To take the first steps in making a 3D visualization in an environmental setting, there is a very good course on Udemy:
In 1-2 weeks (non-stop) time, you will be able to make a basic ecosystem in Blender.


To find out more about this master project, please contact Prof Dr Johan van de Koppel ( 

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