Matthias Meyer-Bender
Matthias is a predoctoral fellow at the European Molecular Biology Laboratory (EMBL) in the groups of Wolfgang Huber and Sascha Dietrich. Prior to joining EMBL, he obtained a BSc and MSc in bioinformatics at the Technical University of Munich and Ludwig-Maxmilians-Universität Munich. His current research involves analyzing highly multiplexed fluorescence microscopy images of Non-Hodgkin B cell lymphoma.
Sessions
Recent advances in spatial proteomics have enabled highly-multiplexed profiling of tissues at single-cell resolution on an unprecedented scale. However, various technical challenges such as autofluorescence, the sheer size of the images, and batch effects across samples impede the automated and reproducible analysis of antibody-based imaging approaches. To address these issues, we developed spatialproteomics, a Python package designed to streamline the (pre-) processing of multiplexed imaging data. Spatialproteomics provides a unified API for various image processing algorithms, ranging from nuclei segmentation to cell type prediction, and supports data visualisation through an easy-to-use plotting interface. For scalability, spatialproteomics leverages xarray and dask, enabling to lazy-load and process larger-than-memory data in parallel. Finally, we ensure interoperability with existing scverse tools to facilitate spatial downstream analyses. In summary, spatialproteomics offers a fast and flexible alternative to rigid image preprocessing pipelines, thus facilitating rapid-prototyping and custom preprocessing for highly multiplexed imaging data.