The Challenge

The client wanted to use spatial single‑cell transcriptomics to study the molecular histopathology of chronic inflammatory bowel disease. No benchmarked workflows existed, and the technology required sophisticated analysis.

Our Approach

We re‑annotated spatial datasets, developed a tailored workflow and performed analyses to uncover inflammatory signatures and cell‑cell communication.

• Data re‑annotation & niche discovery: Re‑annotated public spatial transcriptomics datasets, identified spatial niches and performed trajectory analyses.
• Workflow development: Built an end‑to‑end workflow including gene‑expression analyses and cell‑cell interaction modelling, and optimised it for reuse across diseases.
• Analysis & optimisation: Analysed cell‑communication networks, spatial signatures and trajectories to reveal disease mechanisms and potential targets.

The Outcome

• Delivered a customised spatial transcriptomics workflow.
• Confirmed the relevance of the technology and provided new insight into disease progression and potential drug targets.
• Produced a workflow that can be applied to other disease areas.

Why It Matters

Spatial transcriptomics adds a new dimension to cellular analysis. This project shows how custom workflows can unlock the value of spatial data to reveal disease mechanisms and support drug discovery.