Exercise 2: Convert Images Locally

Activate the conda environment:

source /scratch/miniforge3/etc/profile.d/conda.sh      # source the conda binary
conda activate eubizarr                                # activate the eubizarr environment

• You could list all the available conda enviroments using conda env list.
• Always check you are using the correct conda environment.

Create a results folder:

mkdir ~/results_local                                              

• The ~ expand to your own home folder, e.g. /home/YOUSUSERNAME/
• On BAND, you only have write permission to your home folder and /scratch
• You can create any folder under ~ or /scratch to store results.

Run the conversion

eubi to_zarr /scratch/ngff_workshop/examples/pff ~/results_local   

• These steps convert all images in the pff folder into Zarr format and save the results in ~/results_local.
• The conversion only uses 1 node.
• The conversion runs on the same node where your BAND desktop is running.

Check the results

List the contents of the output folder:

ls ~/results_local

Expected output:

• There should be 7 Zarr folders