nf-core/mcmicro and nf-core/molkart: What we learned from bringing imaging pipelines to nf-core

Imaging-based spatial omics technologie are becoming widespread and efficient, and large amounts of data are being created every day. High-throughput, scalable, adaptable, and reproducible data analysis is becoming a key challenge to unlock the full potential of existing and emerging technologies. Leveraging nf-core as the framework, we have developed two highly-multiplexed pipelines: Molkart, a pipeline tailored for combinatorial smFISH Molecular Cartography data, and an adaptation and expansion of MCMICRO, the multiple choice microscopy pipeline for high-throughput processing of large Bioformats-compatible highly-multiplexed antibody-based imaging data. We present pipeline update plans, use cases and challenges we faced along the way.