Bringing imaging pipelines to nf-core: MCMICRO and molkart

Unlocking the full potential of emerging imaging-based spatial omics technologies requires high-throughput, scalable, adaptable, and reproducible data processing. As the spatial omics field continues to grow, the need for workflow standardization that ensures long-term sustainability is becoming increasingly important. The nf-core community, tools and guidelines provide a strong foundation to accelerate spatial omics workflow development. We present two highly-multiplexed pipelines: Molkart, a pipeline tailored for targeted spatial transcriptomic data (Molecular Cartography, MERSCOPE), and an adaptation and expansion of MCMICRO, the multiple choice microscopy pipeline for processing of large Bioformats-compatible highly-multiplexed antibody-based imaging data.