2015-10-27 Tuesday Team Meeting
Dundee: Petr, Will, Dominik, Colin, Gus, Melissa, Mark, Simon, Roger, Simone, Balaji, Jean-Marie, Jason, Stick, Chris, Remote: Sebastien, Eleanor, Kelli, Ian, Jean-Marie, Ola, David, Helen,
Agenda - 2:30pm Start
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
OMERO
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5.2.0 (J-m)
- Last build just triggered, last few PRs merged this morning.
- QA bug (not regression)
- RC2 prepared for tomorrow
- Docs testing tomorrow
- Cleaning sections for Java Gateway
- Helen: well on track - most PRs open, Help docs work in progress
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Regions v2 (Josh)
- Mark: quiet right now, Roger working on XML
- Next week - some ideas for discussion
- JM: need to consider containers etc. for API
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5.2.0 (J-m)
Bio-Formats
Glencoe Update (Chris)
- omero_marshal tweaking based on feedback
- permissions bugs need more investigation (loaded / unloaded data not as expected)
- Need to discuss how much is marshalled, how to return unloaded vv missing data
- Raise conditions on linking of Annotations can be tricky when saving
- MapAnnotations are ordered, don’t match existing data structures in languages
- Harder to search, serialise etc.
Repositories
- Virtual Microscope/teaching
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IDR Project
- Eurobioimaging list e-mailed
- Mills Observatory “Inner space, outer space”. GRE outreach launched last night.
FLIMfit/OPT (Ian)
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Presentation by Ian for the latest features.
- Quickly cover existing functionality, then plate at end
- FLIM images decay curve of image after laser pulse
- Load Dataset from OMERO into FLIMfit.
- Every pixel has a decay curve, made up of several parameters - lifetime etc.
- Can see a false colour image of each parameter, can be saved back to OMERO.
- New: Plate data from our open-source plate reader, based on micromanager.
- Plates saved as OME-TIFF, uploaded to OMERO, read via FLIMfit
- Can choose not to load all wells, field of view etc (checkbox list)
- IRF is a text file attached to plate, can be picked in FLIMfit
- Can see all false colour images in plate after fitting
- Also overlay a ‘heat map’ of each parameter in the plate and save these as a new image in OMERO.
- This will work with any plate data that has modulo-along-T data.
- JM: could save heat-map or thumbnail view as another Plate/Run?
- Ian: these are not very big images.
- JM: Larger plates with lots of data could be slow to access all data remotely.
- Jason: where’s your lib for writing OME-TIFF
- Ian: on github Open FLIM HCA?
- Ian: Other code in micromanager codebase, we have examples of use
- Gus: Releasing this soon (update docs)?
- Ian: Prefer to hold off until we have better data for testing and screenshots.
- Petr: Anything new to update testing scenarios?
- Ian: yes, previously we’ve used multiple OME-TIFFs with row/col etc in image names, stored in Datasets.
- Ian: Need to ‘publish’ partially-acquired plate with missing data etc. Do we edit the original data or (Josh’s suggestion) we have placeholder thumbnails for missing data.
- Jason: can we move some of this functionality back to OMERO server?
- Ian: Need to split UI and processing functionality. Currently users work with files with data in hand, remote desktop to processing machine.
- Remote access to data on OMERO is slow, but not a blocker since processing time or even loading data locally is also slow.
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Presentation by Ian for the latest features.
Other consortium timelines (5 minutes)
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)
- Thanks to those who helped with poster presentations yesterday
- Probably need a new poster soon, with IDR and BF work
- Post-5.2.0 discussion next Wednesday 1.30. Meeting room and food booked