2019-03-05

Dundee:

Remote: Josh, Seb, Frances, June, Will, Melissa, Chris, Dom, Liza, Simon, Mark, Riad, David, Emil

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In:

  • Frances: prod65 in two-ish weeks with two new studies

  • Seb: experimental IDR openmicroscopy m3 build, seems to be

    working

• Data-Out

  • Riad: openmicroscopy m4 running in Travis, reduces boilerplate

    configuration including in CI environments

• Glencoe

  • Chris: Internal OMERO backbone services running (without Ice),

    new version of Vertx, using async workers. Waiting for OME to move to Spring 4 before code can be cleaned up. Investigating Hazelcast distributed maps for cross-process caching.

  • Now looking at microservices especially queries for thumbnails-

    all Hibernate queries will be read-only.

• Community

  • HCA (Josh): metadata team has gotten back about validation, want

    a spreadsheet of files with information on required validation. RFC is open, but no comments yet.

  • HDF5 (Josh): visit at EMBL, met with several developers using

    HDF5 and Imaris, potentially other formats, may or may not become an OME library.

1. AOB

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

• Will: 5-minute demo of iviewer ROI loading by tiles.

  • Riad: Could use heat-maps instead of numeric counts of ROIs

    in a region when too many to display?

  • Will: Main restriction is lack of ability to query location

    information for ROIs

  • Chris:

    https://openlayers.org

    • Even tile-based loading is likely to be too slow with many

      ROIs on multiple planes. Might be acceptable with vector ROIs but not with Masks.

    • Queries probably end up being too case-specific
  • Jason: Community will want support for very large number of

    vectors and Masks

  • Summaries, bounding boxes, centers of mass, density maps (of

    cell type, etc)

  • Close to having an API defined. Then could use postGIS or PSQL

    geometry to store this information. Or maybe a file.

1. Main Topic

(20-25 minutes plus 15 minutes questions max) (Josh)

OMERO Release Schedule Proposal

• M3: decoupling Feb 27

• M4: indexer Mar 15

• M5: insight Mar 22

• M6: Matlab Mar 29

• M7: Bio-Formats 6 Apr 06

• First RC Apr 13

• Weekly releases until 5.5.0 is out.

• Note:

  • Awareness of workshop (as a deadline)

  • Blogging & communicating to developers

Out of scope but in follow-ons:

• Python3 + No Ice

• Microservices