METABRIC-MX
Jun 1, 2024
·
1 min read
METABRIC-MX (Multimodal eXplorer) is a platform for processing and analysing Xenium breast cancer spatial transcriptomics data from the METABRIC cohort. The pipeline handles:
- Multi-modal registration: Aligning metallomics, immunofluorescence, H&E, and Xenium data into unified SpatialData/Zarr objects
- Cell typing: Automated annotation using CellTypist with the Chen.pkl model trained on 600k+ cells
- Batch correction: Harmony and scVI integration across tissue microarray cores
- Spatial analysis: KNN smoothing, neighbourhood composition, and immune niche profiling
Authors
Anthony Baptista
(he/him)
Senior Postdoctoral Research Fellow
I am a Senior Postdoctoral Research Fellow in Cancer Bioinformatics at King’s College London,
working in the Grigoriadis group within the School of Cancer & Pharmaceutical Sciences.
My research sits at the intersection of spatial transcriptomics, graph theory, explainable AI,
and tumour microenvironment biology, with a focus on breast and liver cancer.
I co-lead the KCL Spatial Biology Facility
and co-organise the Alan Turing Interest Group on Topology and Geometry for Data.