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Imaging Working Group Minutes

Thursday, 2021/10/21

10:00 am ET

Attendees:

Terrell Russell, Alan King, Kory Draughn, David Fellinger, Josh Moore (Dundee / OMERO), Valeria Mazzano (NYU Langone), Ken Langley (UNC SOM-IT), Rolf Harkes (NKI - Netherlands Cancer Institute), Marjolijn Mertz (NKI - Netherlands Cancer Institute), Michelle Itano (UNC Microscopy), Mathias Hammer (UMASSmed), Nirav Merchant (CyVerse / UArizona), Caterina Strambio-De-Castillia (UMass Medical School), Krenchicky Castro (NYU Langone), Ken Ho (Crick, UK)

Minutes

  • NGFF next meeting is December, but not scheduled yet
    • If interested, get in touch with Josh Moore
  • What steps can we take to prepare the ground for when someone is ready to type/code?
    • Possible technical presentations of existing stack(s)
    • Tiny Proofs of Concept, scratch a simple itch, see if any patterns emerge
      • Via OMERO API - then talking to iRODS API
  • Seeking clarity on primary use case / pain point for this integration
    • Adding lifecycle planning to OMERO data
    • Adding imaging client/tooling to iRODS data
    • Sharing data at scale, across users / labs / institutions
    • Registration of existing data in iRODS, then add tooling (OMERO)
    • Retention (aka can we ever delete this stuff? Who decides? When?)
  • CyVerse, currently holding a 100TB cache for OMERO… purged over time
    • Tagging-based awareness between systems
    • Could be a use case for iRODS Storage Tiering
    • HPC is at TACC (Texas), staging is in the background / automatic / local
    • Michelle: even just migration between workstations would be useful
    • During training... iDrop on workstations into shared space, overwhelmed network
  • TODO:
    • Terrell to make a new picture (v2, with more EventLog from OMERO -> iRODS)
    • iRODS to learn some OMERO API
    • Terrell/Josh - OMERO event, trigger tiny (Python) script to inform iRODS of new file
      • Tag in OMERO as 'registered'
      • Unit of work is either single file, single directory, or list of specific files
      • Parameter could be 'where in iRODS', rather than hard-coded
      • Parameters could also be users/permissions/metadata
    • Any code can live in this working group repository
      • We'll plan to use GitHub issues
  • Next Meeting:
    • Jan 2022