Thesis subject
3D analysis of the swimming muscles in larval zebrafish
During development, the axial muscle fibres in the trunk of larval fish change direction to finally form a helical pattern in the adult fish body. However, during these structural changes in the swimming muscles, the larval fish still need to swim properly to eat and avoid being eaten. At what rate do the muscle fibres change direction? Is this a constant rate over the whole length of the body? Or is there a difference between e.g. the tail and the trunk? There are many unanswered questions in this area of research.
Fish larvae are the smallest free living vertebrates. Because of their small size, they experience the water in which they swim as much more viscous than adult fish. Therefore, they swim with higher tailbeat amplitudes and frequencies than their adult counterparts. Their muscles are adapted to this, on all levels from muscle molecules to muscle fibre direction and myosept shape. In the overall research project, we investigate how larval zebrafish use their muscles during swimming, and how this changes as the larval fish develop. A big part of this research is to find out what the 3D arrangement of the muscle fibres is in the first few days after hatching, and how the arrangement changes over time.
In this thesis project, you will analyse two or more light sheet microscopy scans to make a 3D analysis of the muscle fibres of a larval zebrafish. For this project, you will need to program a script to analyse the data, and to quantify the scans in a meaningful way. You will then discuss the functional relevance of the observed changes in the internal muscle morphology for the swimming of larval zebrafish. This may also involve creating a model.
The skills your will be using/learning are: image analysis, 3D reconstructions and visualisation, 3D microscopy scans, programming in Python and statistics.