2018-11-13

Dundee: N/A

Remote: Simon, Frances, JM, Kenny, Riad, Dom, Petr, Josh, Wilma, Seb, Melissa, Chris, Andreas, Emil

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In

  • Bio-Formats 6.0.0-m3 (Seb)

    • Several requests for new functionality

      • Downsampling (pyramids) + writing performance

      • To be tested by collaborators

  • S3 status (Simon):

    • Brief investigation into reading performance problems with

      S3 BioFormats

    • Looking into HPA as a example use-case

    • Josh: Will need a way for OMERO/BioFormats to handle

      authenticated remote URLs, and for OMERO to differentiate between files and remote URLs

    • Seb: Keep all work on mainline branches unless unavoidable

  • bia-tool (Josh):

    • agreed with Ugis in Heidelberg on a the

      blackbox strategy.

    • Now available on

      incubator.

    • Want an OMERO that’s not OMERO, generate thumbnails for a

      directory of images

    • omero render isn’t sufficient

    • Chris: not yet available as a microservice but on the todo

      list. PRs to assist on the way.

  • spacetx-fov-writer (Josh):

    • now works with HCS data (BioFormats 6) to generate multi-FOV

      spacetx datasets. These have been imported into OMERO as well as viewed in starfish notebooks. See current drawing for the grant proposal (going in today)

    • Next step is to generate OME-XML for spacetx filesets

      (companion files for TIFs on disk)

  • IDR 0.6.0

    • Datasets (Frances/Dom)

      • Two datasets for next release, both KLB datasets.

        Currently going into test60

    • Software (Seb)

      • Some bugs in IDR 0.6: OMERO 5.4.9 + BioFormats 5.9.2 +

        IDR fixes + BF6 backports

      • Need to test all existing studies, so far filepattern

        known to be broken

      • Iviewer going in to IDR as alternative (not default)

        viewer

• Data-Out

  • Mark: omero-downloader: Slowed development to stabilize for

    testing for initial release. Petr has started to take a look. Current blockers are licensing question (GPLv2+?), code review, testing/CI, possible move to GitHub in making repository public. Some clear manageable to-do’s identified for subsequent release. Larger issues are: OME-XML is the only metadata export format offered; OME model coverage is light because OMERO’s for import/export is correspondingly light and yet to choose how to improve coverage.

    • Petr: Tested on Mac, no bugs yet!

  • OMERO 5.4.10 and PR freeze (JM):

    • Required to fix Fiji training blocker

    • PR to consider EOB tomorrow so we can release next week

    • Insight version working with smuggler. To be included in the

      coming release

  • Demo slow:

    • JM: Problem reproduced on pub-omero. Seems to be related to

      the permission system admin (light) vs normal user. Doesn’t seem to be related to particular web sections. Mark and Riad investigating.

  • iviewer to be released for next workshop (0.6.0)

  • Cambridge training (JM):

    • Focus on R rGateway so new version to be released before end

      of the month.

    • Training image is currently broken.

    • Dom: Hopefully on CRAN after next release

• Glencoe (Chris):

  • Some OMERO PRs

  • Several BioFormats issues, some already backported to

    open-source

• Community

  • Turku, I2K, Cambridge, workshops

  • Euro-BioImaging EBIB (Josh):

    • Aim is to facilitate communication with industry

    • General willingness to reduce number of new formats and to

      collaborate

    • Need to improve outreach?

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)