Attending: Josh, Will, Frances, Mark, Chris, Simon, Petr, Melissa, Sebastien, Wilma,
David, Dominik, Jason, Jean-Marie, Andreas, Emil,
Start: 2:00 pm
(2-3 minutes each)
Idr0071 needs more testing: Simon:
32 images have excess metadata: Potential workaround
Duplicate Project/Dataset names causing issues
Plan to import then assess
- <img src="../images/2020-06-23-image1.png" alt="zarr schema" style="width:3.34896in;height:1.55926in" />
0a37477… Add alt - Simon working on spec
- Dundee team working on ‘bottom’ path above - GS working on ‘top’ path. - Omero-rois (python, OME team) used in IDR - Omero-roitool (Java, GS) uses existing Java libs - ITK > [<u>inquiry</u>](https://github.com/Kitware/itk-vtk-viewer/issues/315) > about location of spec to add support - From napari zulip, > [<u>https://github.com/tlambert03/napari-omero</u>](https://github.com/tlambert03/napari-omero) - Good to support masks - Discussion with Erich Bremer - Stony Brook. - Mostly were discussing the intersection of RDF with binary > data - See [<u>\[2005.06469\] Representing Whole Slide Cancer > Image Features with Hilbert > Curves</u>](https://arxiv.org/abs/2005.06469) - Spatially indexed representation of polygons to overlay > on images - Done via a column store-like representation which could > be used within Zarr. - … > Pathology … > … > DICOM … - But: Was unclear on tile server feature. Upcoming > publication of one (IIF-compatible) which could be > submitted back. Also has an CECOG-like HTTP implementation > for Bio-Formats. - Also, successfully using > [<u>native-image</u>](https://www.graalvm.org) > (from GraalVM) to compile Bio-Formats to native code. - Doesn’t support reflection - manual effort required - Awaiting publication etc.
VMWare hypervisor and firmware updates
require VMs to be updated at our leisure (proposed timescale: over two week period following start of work by UoD IT)
Mail migration: Last week’s testing passed, list migration
underway this week.
Emil, Wilma to latter? Maybe Kevin? Happy to go with what works for Glencoe. Current omero-team members are Chris, Melissa, Stick.
Bioformat2raw work on Plates and Memoizer
n5/zarr usage in Java investigation
Workshop videos? July?
JM: video recording? Quality? zoom vs OBS etc?
Jason: needs discussion later
Community meetings? More frequent meetings suggested.
Get some more work done first
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
If desk is taped off, choose another
If you want to work in office, let Jason know.
(20-25 minutes plus 15 minutes questions max)