Wednesday, 12th of February at 2:00 pm – 2:40 pm
Chair: Bertram Bengsch & Henrik Mei
Denis Schapiro
Institute for Computational Biomedicine and Institute of Pathology
Heidelberg University Hospital
From oncology to cardiology: Spatial omics technologies for topographic biomarker discovery
With improvements in speed and amount of data that can be collected from tissues, data processing and analysis have become the major challenge for spatial biology. Therefore, we developed the open-source histology topography cytometry analysis toolbox (histoCAT), which became the first software specifically tailored to analyse highly multiplexed images. HistoCAT includes advanced machine learning approaches and basic statistical methods integrated in an interactive desktop application. Recently, we have developed a scalable and modular computational pipeline (MCMICRO) enabling the analysis of a variety of highly multiplexed spatial technologies for proteomics (antibody-based) and transcriptomics. We demonstrated the use of MCMICRO on dozens of tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software. In the second part of my talk, I will cover the Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard as well as our spatial power analysis framework to improve experimental design strategies. Lastly, I will highlight how we utilized the developed tools to process data with a focus on myocardial infarction and how we are currently building a translational center for spatial profiling (Translational Spatial Profiling Center – TSPC).
Biosketch
Dr. Denis Schapiro is Managing Director of the Translational Spatial Profiling Center (TSPC) and Research Group Leader at the Heidelberg University Hospital focusing on spatial omics technologies and analysis. He is also the current president of the European Society for Spatial Biology (ESSB) e.V.
Before moving to Heidelberg, he was an Independent Fellow at the Laboratory of Systems Pharmacology at Harvard Medical School and the Klarman Cell Observatory at the Broad Institute where he was a Damon Runyon Quantitative Biology Fellow mentored by Prof. Peter Sorger and Prof. Aviv Regev.
Denis obtained his PhD from the University of Zurich and ETH Zurich in the laboratory of Prof. Bernd Bodenmiller where he worked on Imaging Mass Cytometry and corresponding analysis tools focusing on highly multiplexed image analysis. Prior to this, he received his diploma (Dipl. Biol. (t.o)) at the University of Stuttgart and Harvard Medical School working with Prof. Peter Sorger and Prof. Alfred Goldberg.