Access IDR data available on S3

[jburel]

Several of the IDR studies are now also available on S3 see https://idr.github.io/ome-ngff-samples/. Note that some from the BioImageArchive are also available at https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/bia_examples.html

We have prepared examples notebook around some of those studies

• https://github.com/ome/omero-guide-python/tree/master/notebooks Look for notebooks with zarr in the file name
• https://github.com/ome/omero-guide-cellprofiler/blob/master/notebooks/idr0002_zarr.ipynb: example using CellProfiler
• https://github.com/ome/omero-guide-ilastik/tree/master/notebooks: example using ilastik
• https://github.com/ome/omero-guide-fiji/blob/master/notebooks/imagej_python_zarr.ipynb example using imagej python

We are also preparing material for https://github.com/IDR/idr0125-way-cellpainting/tree/main/notebooks

we have more examples if required

[gwaybio]

Hi @jburel - Thanks for providing these resources! Sorry for not responding sooner, I just saw this issue now.

We are currently not focused on IDRstream in the short term, but hope to dive back in once we have more clarity on a couple outstanding items, hopefully mid-year.