FOCUS: end-to-end preprocessing, alignment and resolution-matched integration of spatial multi-omics data

Integrating spatial multi-omics data requires coordinated preprocessing, cross-modality alignment and feature registration across modalities that differ in file format, coordinate system and spatial resolution. No existing tool addresses this pipeline end-to-end from raw experimental files till aligned data object. We present FOCUS, an open-source Python package that takes raw data from spatial transcriptomics, mass spectrometry imaging, Raman spectroscopy imaging and brightfield or fluorescence microscopy through modality-specific preprocessing, interactive spatial alignment and resolution-matching registration to a unified MuData object, driven by a single configuration file. Its modular, registry-based architecture allows straightforward extension to additional modalities. FOCUS is accessible via a command-line interface, a browser-based GUI and a Python API.