Helium-Ion microscope

An extraordinary PhD project

Cooperation between a university and a hospital.


During the Interreg5a project Celltom, some of the partners met and learned about new microscopic technologies and their application to biological samples. The project ended, and the knowledge about the technology evolved in the heads of some partners.

During her medical work, Vibeke from the University Hospital of Southern Denmark is interested in understanding the development of Inflammatory Bowel Disease (IBD). The knowledge is incomplete but likely involves an interaction between factors such as diet, gut microbes, and genetic risk factors. Understanding how these factors work together is key for understanding modern world diseases. She knows Jakob from the Mads Clausen Institute and remembers his presentations about the Helium Ion Microscopy (HIM), a new advanced technology that enables visualisation of microbes and human cells at high resolutions. The technique allows resolving fine structures without the need for coating, e.g. used in electron microscopy. Another technique is of interest, and this is confocal immunofluorescence microscopy, where Aalborg University can contribute.

For the first time, the research team plans to visualise the interaction between microbes and host-epithelium structures with advanced microscopy techniques.

The idea results in a PhD project

Vibeke at the University Hospital of Southern Denmark has the idea for a PhD position, and the partner from the Mads Clausen Institute of SDU in Sønderborg joins in with their expertise in advanced microscopy, namely Helium Ion microscopy. The partner from Aalborg University will also contribute with specialist knowledge on confocal immunofluorescence microscopy and the University Hospital of Southern Denmark with their expertise in pathology.

Importance of knowing each other

For these partners, it was precious that they met before and had time to learn about the expertise of the others in the Celltom project. This helped to find the partners and get the idea for the PhD project. Over time the partners had the chance to build up trust, which encouraged them to start something new.

Benefit for the PhD candidate

The PhD candidate has the advantage that she/he can work truly interdisciplinary and benefit from highly experienced partners. There is also a challenge involved in having to learn the details of two fields. But that is the breeding ground for innovation.