2020-04-21

Attending: Petr, Josh, J-m, Frances, Mark, June, David, Dom, Seb, Simon, Jason,

Liza, Will, Melissa, Wilma, Chris, Emil, Andreas

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR

  • Simon: Working on a second production deployment

  • If starts OK, will look at network swap

• IO: Josh:

  • Friday - plan to demo a set of IDR images being opened via

    napari from s3.

  • Zarr in minio: format, etc.

  • bioformats2raw: layouts, etc.

  • Need to keep various repos in sync as we evolve our new zarr

    format.

  • Seb: remember to record the demo.

  • JM: looking at images from idr0062 - 5D. Comparing metrics from

    opening with raw TIFFs with Pillow, zarr, h5 etc.

  • Will: demo napari running on remote machine?? Josh: follow-up

    after meeting

• SA (learning/mail)

  • We have a final GPFS quote

  • VMWare licenses still valid for 11 months

  • We need somewhere to document licenses and renewal dates

    (calendar….?)

    • Josh: previously

      https://trello.com/b/GdVexOBr/software-licensing-no-keys-please

    • Seb: need something with notifications

• Glencoe, Chris:

  • Bioformats2Raw progress

    • Issues with incomplete tiles/padding

    • Fixes and release unlikely in the short term

    • Will set up our own n5-zarr repo with SNAPSHOT builds

    • Bio-Formats fixes from 5.6.1 feedback

• Community

  • OME Mtg

    • om.org website updated

    • Latest draft

      agenda

    • Speakers contacted re:video recordings

    • Trial run– BioImagingUK mtg this week, breakouts next week

    • Deciding on video hosting soon.

    • This week: Schedule recording of talks

    • Today - test meeting

    • Strategy docs for breakout sessions

    • Workshops - prepare our own from training workshops

      • Also invite community, e.g. Glencoe and others

• IO Demo:

  • Remote desktop available? MyBinder with napari? VNC UI update

    choppy

  • What is goal of demo?

  • Want to get consistent measure of performance.

  • JM: can demo loading of zarr/zip/tar from file-ann on Image

    • Can’t load zip from minio

  • Simon: demo napari loading from minio.

  • Jason: we have Windows remote desktop available

    • But blosc etc not tested on Windows

  • Chris: who has best bandwidth connectivity?

    • Chris: I can run locally, if Will gives me instructions.

    • Can we run on Windows?

  • JM: which files to use - idr0062

  • Seb: idr0044 2k x 2k x 1k…etc.

  • Josh: converting using Docker running on server.

  • Will: Using nested chunks?

  • Josh: Seeing RecursionError when loading over s3.

  • Seb: maybe 1 million chunks in idr0044

  • Josh Image:3428066 - fails with nested OR un-nested chunks

1. AOB

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

1. Main Topic

(20-25 minutes plus 15 minutes questions max)