Cryo-electron microscopy (cryo-EM) has become an indispensable tool in structural biology, enabling high-resolution single-particle analysis (SPA) and cryo-electron tomography (cryo-ET), as well as facilitating research in the emerging field of lipid nanoparticle (LNP) characterisation.

Although Cryo-EM @ LU has a growing user base and robust sample-preparation workflows, its data-processing infrastructure is incomplete. The lack of an integrated, automated pipeline complicates user access, delays results and reduces the facility’s overall efficiency.

This project therefore aims to design, implement and validate a unified data processing pipeline that supports SPA, tomography and LNP analysis. This will include the automation of data transfer from the Falcon 4i offload server to high-capacity storage, real-time pre-processing via CryoSPARC Live and the structuring of data for routing to temporary and long-term storage for remote access. Dedicated workflows for tomography and LNP projects using IMOD, Warp/M, Dynamo and specialised particle detection tools will also be established.

A strategic collaboration between the cryo-EM facility and CIPA (InfraVis, Lund University) will provide expertise in advanced image analysis, workflow optimisation and coordinated user support. Furthermore, the project strengthens cross-border collaboration by aligning methods with the Danish QIM initiative and cryo-EM hubs in Copenhagen and Aarhus, thereby contributing to a more integrated Nordic imaging ecosystem.

The resulting infrastructure will deliver a stable and scalable system that will support diverse scientific projects, ensure reproducible workflows, enhance data integrity and strengthen the regional cryo-EM landscape. Ultimately, the project will improve the user experience, increase accessibility and accelerate scientific output in the life sciences across the HALRIC network.