Tutorials

Each tutorial runs the full LYNX pipeline on a different multi-modal spatial application.

• Liver — Xenium transcriptomics + DESI metabolomics — Xenium spatial transcriptomics + DESI metabolomics; principal curve trajectory (periportal → pericentral zonation) with cell–cell interactions.

• Breast — Xenium transcriptomics + H&E histology — Xenium spatial transcriptomics + H&E histology; principal tree trajectory (from an immune niche to either DCIS or invasive tumor cores).

• Thymus — spatial RNA + protein (CITE-seq) — spatial RNA + protein (CITE-seq); principal curve trajectory (cortex → medulla axis).

• Liver — Xenium transcriptomics + DESI metabolomics
• Breast — Xenium transcriptomics + H&E histology
• Thymus — spatial RNA + protein (CITE-seq)