Advancing Whole Mouse Brain Vasculature Datasets for Blood Flow Simulation
Masterthesis / Biomedical Engineering / Student Project
Status: Open
Time frame: September 2025 - February 2026
Advancing Whole Mouse Brain Vasculature Datasets for Blood Flow Simulation
Project background
Regulating blood flow is vital for healthy brain function, and its disruption is linked to neurodegenerative diseases, making it crucial for diagnosis and treatment. Whole mouse brain vasculature datasets offer valuable insights into blood flow regulation, but available datasets [1],[2] still come with major limitations, e.g., missing surface vessels, artifacts, and unclassified veins and arteries. All these aspects are essential for accurate whole-brain blood flow simulations, which would allow us to deepen our understanding of vascular topology and advance diagnostic and therapeutic approaches in neuroscience.
Possible projects
1) Enhancing whole brain vasculature datasets (Python)
a) Surface vessel tracking, reconstructing, and registration for different brain areas [3,4] (geometry, image registration, machine learning)
b) Improve Segmentation of specific brain regions (Image processing)
2) Blood flow modeling in realistic microvascular networks (Python)
a) Inverse modeling (tuning of diameters & boundary conditions by incorporating in vivo data) [7], [8].
b) Investigating the role of reduced vascular density in different brain areas [5], [6].
All projects are purely computational. The precise topic can be refined based on the student’s interests and current necessities. The tasks range from simulation studies to the development of novel computational approaches.
Requirements
You should be motivated to work on interdisciplinary research questions and able to work and acquire knowledge independently. A background in biomedical engineering, computer science, or applied mathematics is preferred. Knowledge in at least one of the following areas—geometry, image processing, machine learning, or fluid dynamics—is advantageous. Experience in programming (Python) is required.
The Institute
You will be a member of the Cardiovascular Engineering research group (Chair: Prof. Dr. Dominik Obrist), which works on various topics related to biomedical flow systems and offers a creative and international working environment. The group is part of the ARTORG Center for Biomedical Engineering Research, which is the University of Bern´s transdisciplinary Center of Excellence for medical technology research. Its mission is to tackle unmet clinical needs and envision future challenges in diagnosis, monitoring, and treatment to create viable healthcare technology solutions with imagination, agility, and purpose. Its projects run from discovery and basic research to clinical translation.
Supervisor: Dr. Sofia Farina
Departement: Cardiovascular Engineering Research Group, ARTORG Center for Biomedical Engineering Research
Language: English
Contact: sofia.farina@unibe.ch
Application: If you are interested in the topics outlined above, please contact Dr. Sofia Farina (sofia.farina@unibe.ch). Please include the following information in your mail:
1) What kind of position are you interested in (including start date and duration)
2) A few words about your motivation
3) The topic that interests you the most
4) Comment on your prior experience in modeling and programming
5) CV
6) Full transcripts from studies
References
[1] X. Ji, T. Ferreira, B. Friedman, R. Liu, H. Liechty, E. Bas, J. Chandrashekar, and D. Kleinfeld, ‘Brain microvasculature has a common topology with local differences in geometry that match metabolic load’, Neuron, vol. 109, no. 7, pp. 1168–1187, 2021.
[2] C. Kirst et al., ‘Mapping the fine-scale organization and plasticity of the brain vasculature’, Cell, vol. 180, no. 4, pp. 780–795, 2020.
[3] B. Xiong et al., ‘Precise cerebral vascular atlas in stereotaxic coordinates of whole mouse brain’, Front Neuroanat, vol. 11, p. 128, 2017.
[4] S. Ghanavati, J. P. Lerch, and J. G. Sled, ‘Automatic anatomical labeling of the complete cerebral vasculature in mouse models’, Neuroimage, vol. 95, pp. 117–128, 2014.
[5] F. Schmid, G. Conti, P. Jenny, and B. Weber, ‘The severity of microstrokes depends on local vascular topology and baseline perfusion’, Elife, vol. 10, May 2021, doi: 10.7554/eLife.60208.
[6] F. Schmid, P. S. Tsai, D. Kleinfeld, P. Jenny, and B. Weber, ‘Depth-dependent flow and pressure characteristics in cortical microvascular networks’, PLoS Comput Biol, vol. 13, no. 2, Feb. 2017, doi: 10.1371/journal.pcbi.1005392.
[7] R. Epp, F. Schmid, and P. Jenny, ‘Hierarchical regularization of solution ambiguity in underdetermined inverse and optimization problems’, Journal of Computational Physics: X, vol. 13, Jan. 2022, doi: 10.1016/j.jcpx.2022.100105.
[8] R. Epp, F. Schmid, B. Weber, and P. Jenny, ‘Predicting Vessel Diameter Changes to Up-Regulate Biphasic Blood Flow During Activation in Realistic Microvascular Networks’, Front Physiol, vol. 11, Oct. 2020, doi: 10.3389/fphys.2020.566303.