2016-06-14 Tuesday Team Meeting
Dundee: Will, Kenny, Gus, Helen, Simon, Colin, Simone, Roger, Balaji, Jean-Marie, June, Ola, Kenny, Petr, Jason, Remote: Josh, Andrea, Melissa, David, Kelli, Eleanor, Seb, Andreas, Ian, Wilma, Chris,
Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)
Agenda - 2:00pm Start
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
Spaces
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Model (Sebastien)
- 5-10min presentation on 2016-06 model
- Changes proposed for 2016-06 from last 6-8 months, Mark, David, Roger
- Namespace unification. Single namespace instead of SAs BinaryFile etc
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Class Hierarchies.
- LightSource, Shape and Map are now ComplexType. E.g. use instead of
- MapPairs dropped
- ROI Properties dropped: namespace, line ending enums etc
- Folders - top level element - Contains ROIs, Images
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What’s next
- June - release 2016-06 schema
- July - release OME Files C++ 0.2.0
- Aug/Sept - release BF 5.2.0
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Chris: LineCap enums - what’s lost?
- Seb: existing Circle Square linecaps not supported
- These have never been implemented in our clients
- Chris: Need to check if Aperio & Hammamatsu would use these?
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Andreas: Can Folders contain Datasets? Seb: No. But can have tree of Folders
- Andreas: Users ask for custom hierarchy.
- Sebastien: 5.3.0 clients will not support Folder hierarchy for images.
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Metadata (Josh)
- IDR priorities - prototype for tag export, feature calculation for 2 studies,
- Into OMERO tables. Make available to Jupyter analyses.
- More data going in.
- Jason: discussing UI changes for IDR and writing up current work (Thursday)
- IRP from eurobioimaging - http://bio.tools (visitors next week)
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5.3.x Scoping and 5.3.0 (J-M)
- Database change PR opened
- Histogram PR opened for web
- Web api and omero-marshal progress restarted
- Conservatively moving cards to 5.3.0 board
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Outreach (Colin)
- Thanks for presentation videos - more please!
- Helen: unconference notes being organised into pdfs. Preparing blog post
- Colin: Preparing for user training days in Cambridge & Oxford
- May also do some Sysadmin training in Oxford or elsewhere
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Model (Sebastien)
Other releases/upgrades:
- Figure
- Learning
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Sysadmin Lifesci IT provisioned remote processing storage for nightshade.
- Josh: OpenStack training started
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Smuggler (Montpellier)
- Writing docs.
- Thinking of grant for work on splitting imports, as discussed at POTN data pipeline session
- JM: deployment? Andreas: on a few workstations but session timeout too short. Admin wants testing with longer timeout to check on thread counts
Glencoe Update (Chris)
- omero-marshal :more objects mapped
- Key-value search in web
Remove CodomainMapContext from 5.3 OMERO model?
- To be discussed elsewhere
ImageJ backend demo by Balaji
- Use ImageJ on the OMERO server for batch processing of images
- Use OMERO.insight IJ plugin
- Open image - start recorder - threshold image - create ROIs etc.
- Save Macro locally - upload to OMERO as attachment to Datase
- Select Dataset and pick attachment - run script..
- Results are attached to Dataset and user is sent e-mail
- Script creates temp folder, adds images (OME-TIFF) and macro, runs Fiji headless
- Jason: ImageJ “doesn’t scale” (E.g SPW) but still very useful to many users who run ImageJ manually.
- Josh: no security / sand-boxing. Can’t let users run “any macro”.
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Andreas: Many plugins don’t run headless.
- We would put together macros - don’t let biologists write them
- Is it possible to offload processing to cluster?
- Balaji: looking into this.
- Roger: create a “scripts user” with limited permissions on the server to provide sandbox security?
- Josh: tricky to create a generic solution.
- Jason: we could write up various approaches.
- Gus: users want various permissions for different scripts
- Simon: direct access to data / without ice? Josh: discussed at POTN
- Jason: lets work with a couple of local ImageJ use cases.
- Will: upload new images as new Images in OMERO?
- Balaji - not yet. Just handle new files as attachments.
- Will: Can user choose parameters as inputs for macros?
- Balaji: Not currently - considered a ‘black box’