Dundee: Will, Dominik, Petr, June, Jason, Mark, Riad, JM,
Remote: Frances, Josh, Seb, Andreas, Melissa
Start: 2:00 pm
(2-3 minutes each)
IDR (Prod70) in good shape
Software upgraded and Bio-Formats cache files regenerated
New OMERO 5.5 functionalities available e.g. websockets
IDR metadata: authorship discussion
Standardizing author formatting using MEDLINE/Pubmed style
Study -> 2 Publications
Jason: Use Pubmed-central or Europe PMC style formatting?
cellprofiller, fiji etc
Use readthedocs for easy deployment
configs for myBinder
Josh: Usage statistics?
JM: No, not out of the box
Jason: is important for the project. Use e.g. google
analytics (don’t write our own)
omero-web still stuck on various manage.py-style errors
import statements etc
omero-py testing strategy fairly sound
Decoupling of OmeroPy - all PRs excluded.
PR to remove from openmicroscopy on its way
JM: submodules? Scripts?
Need to decide what we want to keep. E.g. many versions of trac pages?
Can turn-off and enable read-only in short term if needed.
EMBL (CBA/ilastik) & File Formats (Josh)
Last time: pattern files (“star5”)
This time: spatial context - Affine transform etc.
Stitching and overlaying
Example of Affine transform for whole image
what order etc?
Ended up coming back to BDV and a practical use case
Use case Images -> Add metadata -> to IDR
Click on ROI - show in table and vice versa
Can we try to get and IDR dataset into a BDV file
BDVWriter with extended API
Create BDV with OME-XML
Segment image and write back to BDV
Fiji/BF to open - ask which series/segmentations to open
Petr: visiting INDEPTH / Lisbon. Zoom link is a MUST (2/Sep)
4-6/Sep link will be re-used or needs to be re-issued.
Purchasing another month of webinar zoom
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
(20-25 minutes plus 15 minutes questions max)