Personal tools
  • We're Hiring!

You are here: Home Community Minutes Conference Calls 2013 2013-04-09 Tuesday Meeting

2013-04-09 Tuesday Meeting

Dundee: Chris, Kenny, Jean-Marie, Joyce, Ola, Roger, Blazej, Andrew, Petr, Mark, Elwood, Helen, Simon, Jason, Will Remote: Colin, Josh, Melissa, Ian, Curtis, Kevin, Laura, Mark Hiner

  1. Accepting minutes from last meeting

    • Done
  2. Update on Scifio : Kevin Elicieri and Mark Hiner University of Wisconsin-Madison (45 mins)

    • Goal is to serve as foundation of multiple scientific libraries, bio-formats and more.
    • Components
      • Meta-data format specific inform
      • Checker - compatibility
      • Parser - populate metadata
      • Reader - interpret pixels
      • Writers - bioformat writers, save image datasets
      • Translators - special, convert between 2 metadata types
    • Backwards compatibility is important. Delegate to SCI-fio layer
    • Formats are the top level entity with inner classes for each component (Checker etc.) Multiple translators.
    • Code on github, tutorial component available to familiarize yourself
    • ColorTable for interpreting pixel data, imagelib2.
    • Service: utility class for managing singleton instances
    • Plugins: a format, many in one context.
    • SCIFIO FAQ Page
    • QA
      • Roger: Readers tied to filter metadata core functionality, not sure how writer / reader support multiple translator.
      • Curtis: Each reader for a format populates its specific typed metadata, apng reader -> apng metadata, apng writer requires apng metadata, translator, takes apng metadata to other format metadata. Core metadate image, format spcific metadata all formats implement, returns all the basic stuff, dimentional, pixel type. Not which microscope was used, sufficient for many writers, implicit translation for each format, from image metadata to fomrat maetadata. Format specific does nto apply, to capture more, define translators.
      • Josh: DICOM to astronomy metadata, will checker fail / parsing?
      • Mark: translator service provides convenience methods, request service to translate between formats. Looks for direct translation.
      • Kevin: ImageJ Fiji, medical imaging formats.
      • Jason: Practical examples where there would be a win?
      • Kevin: Medical imagery and tomography. 1st phase is architecture grant. 2nd phase is to find use cases.
      • Imaging: tomography, DICOM, nifti (neuro-imaging): beyond: astronomy, crystallography
      • Jason: scijava (from Dresen Hackathon)
        • incl. IJ2 context, Roger’s ROI proof-of-concept
        • Discussion in Paris?
        • Chris: reproducing IoC framework in Java?
          • Curtis: found ourselves re-doing it multiple times
          • sezpoz/eventbus encapsulated. Could possibly swap it out?
          • already cut 1.0.0, semantic versioning
          • Chris: third-parties won’t be looking at scijava, will more likely be using Spring, Guice, etc.
          • OSGI scary, but (Josh: jar hell)
  3. FS update (10 minutes) 15:28 UK

    • Josh: Brief summary email, demo 3 & 4 plan.
      • Plan for testing for Petr.
  4. Glencoe Update 15:29 UK

    • Chris: HCS dataset published, 2nd set of work in progress. 1000s of genes, 100+ gigs of data.
    • Chris: Hopefully couple of PRs this week with web infrastructure related code.
  5. Satellite Update (every month) 15:32 UK

    • Ian: looking at changing ome-tiff modulo. Is annotation likely to make it in?
      • Chris: already in current release
    • Ian: Standardize around modulo along T?
      • Jean-Marie: no modulo annotation created from sdt at import.
  6. Any other business (<5 mins) - 15:36 UK

    • Formats documentation release schedule & url decision
      • Helen: seems to have stalled. Getting rid of plone doc for xml model.
      • Sebastien: Just need promotion of format release job and setup apache redirects.
      • Andrew: apache config commented out, folder name is formats, needs changing?
      • Sebastien: Menu change in omero documentation and bio-formats documentation.
      • Andrew: Link checker against rest of the site. Tomorrow.
    • Other release/version questions from devteam
      • Jason: Go with 4.4.7 for now?
  7. Done: 15:45

  8. Dundee: PiCLS Symposium 2013 - Sponsorship

Document Actions