Exercises: GPU-accelerated image processing on HPC#

clesperanto & cupy benchmarking#

On the Taurus cluster you have access to powerful NVidia A100 GPUs. Upload an run the benchmarking notebook from the cupy session and compare the performance of the cluster’s GPU with your local GPU.

Bio-image Analysis workflows on HPC#

Upload a tif file from this zenodo repository to the project space at the cluster. Program a Jupyter notebook using clesperano that segments the nuclei in this 3D dataset (hint 1: generate a notebook on your local computer and upload it to the cluster, hint 2: use top-hat background-removal and Voronoi-Otsu-Labeling). Store the segmentation result on the project space.