Personal tools
  • We're Hiring!

You are here: Home Community Minutes Conference Calls 2016 2016-10-11 Tuesday Team Meeting

2016-10-11 Tuesday Team Meeting

Dundee: Will, Petr, Dominik, Balaji, Jean-Marie, Gus, Mark, June, Roger, Simon, Helen, Remote: Sebastien, Jason, Josh, Andreas, Jerry, Emil, Chris, Eleanor, JB, Liza, Melissa, Ola,

  1. Presentation by Jia-Ren Lin (Jerry) from Harvard (Sorger Lab) - "Probing tumor heterogeneity with Cyclic Immunofluorescence (CycIF), a robust, multiplexed imaging method"

    • Jay Copeland also present.

    • Different type of image - need help to manage data

    • Drug response study - lots of heterogeneity seen using microarray of tissue samples.

    • Existing techniques limited:

      • Mass Cytometry slow & low resolution, Quantom dots limited channels.
      • Quantum dots PE, MultiOmyx (chemical bleach) proprietary
    • Cyclic ImmoFluorescence (CycIF) - single cell multiplexed measurement with cyclic IF

    • Fixed cells -> 1st IF -> Flour inactivation -> 2nd IF -> Flour inactivation

    • Allows to get multiple probes per channel

    • In live cells can inactivate flour with H202 or pepsin (cleaves Abs)

    • Many channels/probes for single cell allows cross-correlation

    • 96-well plates (use 60 wells) 9 rounds of CycIF

    • 3 channels + Hoechst stain per round => 27 channels (Hoechst DNA stain for registration)

    • Import images into OMERO - many channels in web image viewer!

    • Analyse individual cells in images

    • PhenoGraph & Metacluster, Wanderlust algorithm etc.

    • viSNE for visualization of high-dimensional data

    • Can be used to disect and classify drug responses

    • Use High-Res (60x confocal InCell 6000) allows analysis of morphological features (not just intensity)

    • Quantify and cluster morphological features (heatmaps etc)

    • Live cell imaging - use cell-cycle fluorescent markers to probe cell cycle phase

    • RNA FISH CycIF

    • Summary:

      • High content, high resolution, upto 10 cycles in each cell
      • 140 commercial antibodies
      • CycIF for FFPE tissue/slides
      • Pre-stain with 2ndary Abs (use image as background) => Flour inactivation => 1+2 Abs => inact => conjugation
      • CycIF cycles 143 fields, tiled to give Big image, 8 cycles - many channels
      • Image segmentation and analysis of cells
    • Tissue microarray

    • In OMERO, each image in Dataset for each tisse microarray sample

    • Collaboration is important - share data with pathologists etc.

    • Need better image annotations

    • Summary:

      • CycIF can be used in both liquid bopsy & FFPE
      • Can improve traditional IF in FFPE (control autofluorescence & 2ndary background)
    • Will: How to improve web image viewing?

    • Over 4 channels hard to display as RGB

    • Need to be easier to choose 4 channels in web viewer - E.g. assign channel to Red, another to Green & Blue etc.

    • OR calculate summary images

    • Current web viewer - channel names not readable on buttons

    • Too many channels - not scrollable in left of viewer

    • use Z to store each round of cycIF - but can’t name individual channels then

  2. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Files/Formats/OME Files (Sebastien)
        • 5 release tomorrow
        • 5.3 work with Roger on builds etc
      2. Metadata (Josh)
        • New version demo3 with mapr in preparation
        • Jupyter notebooks for IDR - simple analysis examples
        • Copy of IDR available to download via rsync
      3. OMERO 5.3.0
        • SPW display in progress
        • Web apps package renaming ongoing - OMERO.figure nearly done. Push to Pypi
      4. Outreach
        • Balaji presenting at PiCLs
        • GRE symposium
        • Balaji videos in production - Matlab toolbox
    2. Other releases/upgrades:

      1. Figure
        • Waiting for renaming to complete before restarting work
      2. ImageJ
      3. Learning
      4. Sysadmin
      5. Website redevelopment/redesign (Liza)
        • Recent changes to BF and OME files sections. Now working on Products/omero
      6. Smuggler (Montpellier)
        • Met with Icy team to discuss OMERO connection
    3. Glencoe Update (Chris)

      • jpeg XR work, setup on various different platforms.
      • Finalising API - doing everything in memory
      • Preparing to port over to open source
      • Test Datasets will be publicly available
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    • PR merging strategy discussion
    • Improve PR Opening:
      • initiate discussion with relevant people, cc them in description etc
      • List tests added etc.
      • List as much info as possible to help reviewers
    • Improve review:
      • Functional review
      • Code review
      • Everything is public - schedule zoom discussion if needed
      • New Review feature
    • Improve Merge:
      • Need clear statement of ‘Good to merge’
      • Bigger PRs need more reviewers to validate it
      • If mergeable and not merged, bring to attention. E.g. list at standup.
      • If not mergeable, and inactive, Close until ready to review again
Document Actions