Spatialomics is a new service at the Medical University of Vienna.

In this interview, Philipp Velicky, the head of the Imaging Core Facility at the Medical University of Vienna, talks to Baubak Bajoghli, the director of Austrian BioImaging, about his career path and the introduction of spatial omics as a new facility service.

Published: 20.5.2025

Baubak: Could you briefly share your professional background and what led you to lead the core facility at the Medical University of Vienna?

Phillipp: Working at a core facility was definitely not my plan initially—I wasn’t even aware of such career paths. I studied molecular biology at the University of Vienna, did my master’s thesis at Oxford, and then a PhD at the Medical University of Vienna. There I did human placenta research in translational projects, and got in touch with high-end microscopy for the first time. For postdoc, I then got a chance to work in a microscopy development group at ISTA in Johann Danzl’s interdisciplinary group consisting of biologists, physicist, physicians and computer scientists. My project was developing a new microscopy technique for imaging living brain tissue in 3D at nanoscale resolution, and it worked out. After my postdoc, I wasn’t sure whether to start my own group, but realized I loved working with optics, microscopes, and diverse projects. I spoke to people in the field, and coincidentally, the position at MedUni became available. I applied, and I’ve never regretted it.

Baubak: I also enjoy working in an interdisciplinary environment. What was your experience of transitioning from a background in molecular biology to working closely with physicists?

Phillipp: It was a great experience. We were all new in the lab, from physicists to neuroscientists. It took months to find the right language to communicate. One postdoc from Dresden was incredibly patient, explaining the optics to me. I spent months learning how the STED microscope worked—eventually becoming a mini-physicist in optics. We had rotating lab meetings. One meeting there was a computer scientist showing some algorithms for microscope control or for image restoration, and then in the next meeting there was a physicist explaining some new optical pathways for the microscope. So it was always a complete switch of gears, and definitely exhausting, but highly interesting and I enjoyed it a lot.

Baubak: In a multidisciplinary environment, it is also very important that everyone speaks the same language so that people can follow the project.

Phillipp: Yeah, definitively.

Baubak: Now, let’s talk about your current position. You have been the head of the imaging core facilities since 2023. Tell us about your facility and your users.

Phillipp: We serve a broad user base – from first-year medical students, who haven’t ever looked into a microscope and have basically no prior knowledge to advanced researchers developing image processing algorithms, develop new fluorophores and characterize them at our facility. Some days, I have a meeting with a user who says, I want to use a microscope. How can I do that? One hour later, I have another meeting with a senior researcher who wants to develop an experiment with me to characterize the full spectrum of his newly developed fluorophore in living and fixed tissue. So it’s a really, very broad range of users.

Baubak: What imaging technologies do you offer?

Phillipp: In terms of machines, we have pretty much the top systems including high-end confocal microscopes. But our standout is a new multiplexed imaging system from Miltenyi (MACSima), acquired via an FFG infrastructure grant. This system enables antibody-based imaging with over 150 markers on one slide. Now our users, especially the oncologists and the immunologists, can really get a maximum of information out of a single slide. Our collaboration with genomics and proteomics core facilities make multi-omics in spatial biology accessible for our users, where they really can get terabytes of data about transcriptomics and proteomics from their samples. I think this is what makes us unique, at least in the Austrian area and beyond: We have one house with the expertise and systems for all this.

Baubak: Is the system adaptable to other species beyond human and mouse?

Philipp: Yes, the system works with any directly fluorophore-conjugated antibodies. You can buy them or label them yourself. It’s species-independent as long as you have suitable antibodies. The system handles FFPE or frozen sections, ideally 3–5 µm thick. For the spatial transcriptomics there are pre-designed panels for human and mouse. But if you create your own probe sequences, you can use other species too. There are online tools to help build your own panels.

Baubak: Can you do 3D volume imaging with these systems?

Philipp: Not yet with commercial systems. Currently, all these systems, both for transcriptomics and proteomics, work basically with thin tissue sections. Some research groups are working on 3D spatialomics using spinning disk systems, but those setups aren’t user-friendly for core facilities.

Baubak:  Spatialomics is an exciting new technology. Many researchers are unaware of its potential, as well as how to handle the vast amounts of information it can generate. What support do you offer users who are new to spatial biology?

Philipp: Yes, researchers often say that they have seen this publication and used these super 3D spatial tools, and ask how they can do it for their project. We then start explaining to them how the system works and manage expectations. We don’t perform the staining, but we guide users in antibody selection and protocol development. Our technicians run the machines, and we provide training in the commercial analysis software that accompanies the system. Users can use our analysis workstations, which is included in the use of our systems.

Baubak: What’s the range of antibodies users can use?

Philipp: You can start with one, but it’s only worth it if you use more. The theoretical max is over 400, though practically, it’s limited by the plate format. A typical run has 25 – 75 antibodies I’d say.

Baubak: Very helpful. Now, as a researcher, I usually want to obtain as much information as possible from my sample. Can transcriptomic and proteomic data be obtained from the same sample?

Philipp: It’s possible in theory. Of course, you start with the transcriptomics, because the RNA is not so stable. The protocol, however, is not yet standardized. We are currently conducting experiments to develop a protocol and implement this type of analysis, as many users have requested. The problem is that different patents exist for how multiplexing is achieved. Currently, no company offers a solution that works for all cases. Therefore, we as facility try to integrate the two technologies we use for spatial transcriptomics and proteomics. One alternative solution would be to use a series of sections from a sample, using one for transcriptomics and another for proteomics. Of course, it’s not 100% identical, but the data is still very informative.

Baubak: Talking about data, I can imagine that these systems generate a large amount of data. How do users handle and transfer such large files?

Philipp: Indeed, we provide high-performance workstations. We are continuously expanding our IT infrastructure with CPUs, GPUs, and storage. Currently we’re working with IT on a state-of-the-art server-based solution for data transfer. Security is crucial, especially with hospital networks involved.

Baubak: This is very promising. As your facility is associated with Austrian BioImaging, could you please tell us whether you accept external users, including companies?

Philipp: Yes, we do. We differentiate only between academic and non-academic users, not based on university affiliation. Academics from anywhere are treated as internal users. Companies are also welcome, but the pricing and legal processes are different. Recently, we had a startup company using our systems. They can just contact us directly by email or via the Austrian BioImaging platform.

Baubak: We are indeed looking forward to integrating your spatial omics services into our platform.

Thank you for your time.