From Astrophysics to Bioengineering

Jakob Lingg working on his laser scanning microscope to acquire dynamics with high spatiotemporal resolution deep in living tissue (Image: Jakob Lingg)
Jakob Lingg working on his laser scanning microscope to acquire dynamics with high spatiotemporal resolution deep in living tissue (Image: Jakob Lingg)

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Jakob Lingg has been a doctoral candidate at the Graduate Center BioEngineering since June 2019. In his doctoral project, he is conducting research at the Helmholtz Pioneer Campus (HPC) and the Technical University of Munich (TUM) in the field of biomedical imaging. In an interview he discusses the unusual path that brought him to his project, his research and a recent publication in the journal Nature Chemistry. He also gives insights in his interdisciplinary working day and talks about some of the unique aspects at the Graduate Center BioEngineering (GCB). 

Jakob, you're a doctoral candidate in the field of biomedical imaging – what is your project about?

I'm building a microscope which will make it possible to acquire fast dynamics deep in tissue, so we can learn more about the condition of an organism. The project as a whole consists of two parts. First there is the development of the microscope: I've just completed the planning and am now beginning with construction. The second project part concerns spectroscopy, more exactly finding the right fluorescent molecules – i.e. materials that prepare the object in such a way that certain structures become detectable – for application with our microscope. 
By the end of my doctoral studies, I intend to have a completed prototype of the microscope and to be able to list the practical application areas for which this microscopy method is particularly well suited. An example application could be the imaging of blood flow in tumor microenvironments, which could give insights into tumor growth and the impact certain therapies have on tumor growth. 

That sounds fascinating. How did you get to this project? Biological imaging wasn't your field from the very beginning… 

I think my path was rather unconventional. First, I studied physics and then astrophysics, with a focus on cosmology and computational methods. After earning my Master's degree, though, I wanted to do something with a concrete practical application that had an impact on everyday life. At the time I met one of my current supervisors, Oliver Bruns. He was in the process of establishing his laboratory at the Helmholtz Pioneer Campus, where he's now researching new optical imaging methodologies. I was then particularly interested in his work in fluorescence microscopy and spectroscopy, since there are certain overlaps with astrophysics. 

Overlaps between astrophysics and biological spectroscopy? Can you elaborate?

Plenty of things which have been commonly applied for years in optical imaging in astrophysics, for example deformable mirrors or the use of specific spectral ranges, are now slowly finding their way into biological imaging. And there's quite a bit to learn from astrophysics when it comes to processing data as well. The data volumes involved in biomedical imaging are continuing to grow and astrophysics provides methods for processing the large amounts of data collected and for optimizing images. 

Your doctoral project makes it sound like you need a lot of knowledge from biology and chemistry as well?

That's true. At first I didn't know much about the biological aspects. In the meantime though I've been able to learn an enormous amount here – especially because I work in an interdisciplinary team every day and I've attended a variety of different courses. One course at TUM’s university hospital Klinikum rechts der Isar was for example a particularly intensive experience for me. All the other participants came from biology or medicine and I was the only one with a background in physics. It was a big challenge, but in the end I passed the course and learned a tremendous amount. When you learn something new starting from scratch, the learning curve is steep, especially at the beginning. That's something I really enjoy, even if it can mean a lot of work. Luckily, in addition to my two supervisors I also have great colleagues whom I can always ask for help. 

Your working environment sounds really interdisciplinary! 

Absolutely. For my doctoral project I have two supervisors from different academic disciplines: In addition to Oliver Bruns in biochemistry there's also Björn Menze. He is Professor for Biomedical Image Analysis and Machine Learning at Zurich University (UZH) and TUM as well as Principal Investigator at the Munich School of BioEngineering. And in our group at the Helmholtz Pioneer Campus, we have a variety of scientific backgrounds – biology, chemistry, physics, veterinary medicine, information technologies. There's a lively exchange among the various disciplines. 

As a doctoral candidate at the Helmholtz Pioneer Campus and at the Technical University of Munich you had the choice between different graduate centers. Why did you decide in favor of the GCB? 

Well, the subject matter was the most important factor. The GCB is a thematic graduate center for the field of bioengineering and accordingly offers the courses I need – for example the annual summer school and various lecture series. All GCB doctoral candidates work in interdisciplinary projects like I do and come from a variety of different academic disciplines. And I find exactly this interdisciplinary character and the exchange with my colleagues to be incredibly exciting and extremely important. You can say the GCB simply offers the right network. 

You sound satisfied with your decision…

Yes, I'm very satisfied. What I didn't really realize at first and what I now find very positive is the fact that the GCB is a rather small graduate center – everyone is very nice, we're quick to get to know each other personally and we know who's working on what topic. On the one hand we doctoral candidates all have a lot in common, while on the other hand we all have our own specific projects and individual backgrounds. I really notice how widely varied the field of bioengineering is, and input from the other disciplines is always a source of ideas for my own project. For example I have knowledge from astrophysics on processing larger amounts of data, but it's another thing entirely to talk with the GCB doctoral candidates who have studied information technologies and who deal primarily with processing medical imaging data in their own projects.

You recently co-authored a publication in the journal Nature Chemistry – was this something like a milestone in your doctoral project?

It certainly was! The publication arose in collaboration with Emily Cosco and Ellen Sletten at the University of California, Los Angeles (UCLA) and presents a new approach to making biological structures in the short-wave infrared range visible in real time and in color. The project dealt with new dyes, optical systems and the appropriate biological application: These are all sub-areas which play a central role in my doctoral project and as a result I was able to deal with these areas in detail from a different perspective. The publication is also a milestone for me because it marks the end of my initial learning phase; now I can concentrate completely on practical application. 

And what are the next steps now?

I'm pretty much at the half-way point in my doctoral project and am starting to build my microscope prototype. On top of that, soon I intend to participate in a seminar for laser protection officers. And as part of my doctoral project, I want to publish two publications as main author in the areas of optics and chemistry and then submit my dissertation in 2022. 


Webseite Graduate Center BioEngineering 

Webseite of Oliver Bruns research group at the HPC

Webseite on Björn Menze's research

Publication in the journal Nature Chemistry: 

Emily D. Cosco, Anthony L. Spearman, Shyam Ramakrishnan, Jakob G. P. Lingg, Mara Saccomano, Monica Pengshung, Bernardo A. Arús, Kelly C. Y. Wong, Sarah Glasl, Vasilis Ntziachristos, Martin Warmer, Ryan R. McLaughlin, Oliver T. Bruns & Ellen M. Sletten: Shortwave infrared polymethine fluorophores matched to excitation lasers enable non-invasive, multicolour in vivo imaging in real time, Nature Chemistry, 19. Oktober 2020, DOI: 10.1038/s41557-020-00554-5


Julia Knürr


Jakob Lingg