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You are here: Home Community Minutes Conference Calls 2015 2015-10-27 Tuesday Team Meeting

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

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. OMERO

      1. 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
      2. 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
    2. Bio-Formats

      1. 5.1.6
        • Ticking along well - units updates handled OK
      2. C++
        • Transforms groundwork in progress
      3. 5.2.0
        • E-mail sent, mostly on hold for now
    3. 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.
    4. Repositories

      1. Virtual Microscope/teaching
      2. IDR Project
        • Eurobioimaging list e-mailed
        • Mills Observatory “Inner space, outer space”. GRE outreach launched last night.
    5. FLIMfit/OPT (Ian)

      1. 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.
    6. Other consortium timelines (5 minutes)

  3. 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
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