Challenges in spatial transcriptomics - Adipocyte segmentation in bone marrow

Join us for the next BioData Basel meetup, hosted again at the Department of Biomedicine (DBM), University of Basel and University Hospital Basel! Co-promoted with Bits in Bio.

Speaker: Pavel Kos, Computational Biologist at the Department of Biomedicine, University of Basel and University Hospital Basel.

Pavel works on spatial transcriptomics and will discuss the challenges of segmenting specific cell types from spatial data. As a concrete example, he will walk us through adipocyte segmentation in bone marrow, covering U-net model architectures, gradient-based inputs, and preliminary results.

As always, the focus is on methods and technical knowledge, a great opportunity to learn about image-based spatial transcriptomics analysis and exchange ideas across disciplines. No prior experience with spatial transcriptomics required, just curiosity!

Details:

• Date: Monday, 8 June 2026
• Time: 18:00 – 19:30
• Location: DBM, Hebelstrasse 20, Basel (Seminar Room, 2nd floor)

Open to everyone — BioData Basel members, Bits in Bio members, DBM researchers, the DBM Bioinformatics Core Facility, and anyone interested in computational biology. Networking afterwards is welcome!
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