High-Performance Computing (Alice)

This section covers the usage of the Alice HPC cluster for image analysis.

Overview

The Alice cluster provides high-performance computing capabilities for more demanding image analysis tasks.

More on Alice: Alice Wiki

With Alice it is possible to connect to a desktop environment to run GUI applications like QuPath or Cellpose.
Furthermore it is possible to run containers via singularity or apptainer, this allows to run analysis tools in a contained environment. Some examples of container definitions for image analysis tools can be found here:

• github.com/TheJacksonLaboratory/rit-imageanalysis-containers
• git.embl.org/grp-cbbcs/container-recipes

Alternatives

At LUMC there is SHARK

Furthermore SURF provides a national HPC with Snellius