2018-12-04

Dundee: Kenny, Petr, Dom, Mark, Riad, Simon, J-m, June, Jason

Remote: Seb, Josh, Frances, Andreas, Kevin, Chris, David, Wilma, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting - 14:00

• Accepted.

1. Project Status

(2-3 minutes each)

• Data-In

  • IDR

    • IDR 0.6.0 release (Seb)

      • Lightsheet datasets + KLB format + OMERO.iviewer

      • Upcoming: OMERO.iviewer as the default IDR viewer

      • Good community feedback (twitter)

      • JRS: also excitement at conferences to see HPA &

        lightsheet.

        • Great highlight of the technology.

    • IDR 0.6.1 datasets (Dom) - 14:04

      • HPA second batch: unzipped & metadata ready

        • waiting on server, but then done within 2 weeks

        • next batch could conceivably been done base on (new)

          docs

        • JRS: already interest in analysis community

      • Potentially idr0047-neuert-yeastmRNA

      • Prod61 needs a round of iviewer testing

        • Next week (~Thursday) after conferences/workshops

        • J-m to prepare a testing sheet

        • Good to have lots of hands

  • Bio-Formats 6 - 14:06

    • OME-TIFF blog post & dissemination (Seb)

      • Positive feedback; highly retweeted

      • Anatole will try a pyramidal TIFF (+BDV) submission

      • Pete has tried B-F 6 in Qupath; feedback forthcoming

    • Upcoming work (David)

      • Priority is next milestone out before the holidays

      • Including: memory leak fixes, tiling API, tiff writing

        speed, BDV fixes

      • JRS: Vendor interest

• Data-Out - 14:12

  • Mark: OMERO.downloader: Made small improvements in response to

    testing by Petr and Simon. Discovered last Friday that its TIFF export’s pixel data is broken, see card on Trello. If wanting to release imminently then may have to omit image export (easy to hide that option) leaving only binary file download and OME-XML metadata export (tags, ROIs, etc.).

    • Hide option and release

    • Josh: Feature list of what does work would be good, in

      README e.g. “only original file export”, then we can send it to collaborators

    • Seb: thinking about file format support, also makes sense

      per modality

  • J-M:

    • Bumping requirements: dropping Ice 3.5, Centos 6, Python 2.6

      and Java 7

    • Jobs should be coming back to green. Looking into speeding

      up travis.

    • Riad reactivating gradle/Ice 3.7 builds

  • IDR/ROIs: some limitations noticed already. Fixes coming.

  • Training: this week is the last travel (of the year…)

    • Upcoming session in Singapore (March ‘19).

      • General introduction

      • 2 groups of 30 people for 2 days each.

      • Consortium between industry & academic.

      • Project starts in February.

    • Good feedback from Turku. User chose OMERO.

      • Considering a central resource connecting to Helsinki.

• Glencoe - 14:19

  • Working on general bug fixes and extending microservice

    functionality

  • A series of UI fixes (state, refresh, etc)

  • Melissa in Heidelberg for I2K

• Community

  • Mark: Attending the Scottish Microscopy Group Symposium

    tomorrow.

  • I2K: J-m, Josh, Melissa in Heidelberg

  • Cambridge: Petr & Dom

  • Sweden: Jason

  • ASCB

1. AOB

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

• Decoupling of insight; remove deprecation via renaming. Outsight?

• Kenny: huge thanks

1. Main Topic

(20-25 minutes plus 15 minutes questions max)