FGCZ Xenium Implementation: Practical Insights and Recommendations
Paul Gueguen, FGCZ
Zurich Seminars in Bioinformatics
- 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call
Abstract We present the first comprehensive evaluation of the 10x Genomics Xenium platform at the Functional Genomics Center Zurich (FGCZ) since its installation in June 2024. We assess the platform's capabilities and limitations across multiple projects. Our analysis focuses on critical aspects of the spatial transcriptomics workflow, including multi-modal cell segmentation, quality control metrics, and data processing challenges. Through various case studies, we demonstrate how tissue quality and preparation significantly impact analysis outcomes.
We evaluate the platform against existing solutions like VisiumHD and provide practical insights into successful implementation strategies. Our findings indicate that while Xenium offers robust spatial transcriptomics analysis, optimal results require stringent quality control and standardized workflows. We highlight current challenges in the field, including the need for open-source analysis tools and consensus on best practices, particularly for segmentation benchmarking and experimental design.