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You are here: Home Community Minutes Conference Calls 2011 2011-12-20 Tuesday Meeting

2011-12-20 Tuesday Meeting

Attending: Jean-Marie, Will, Elwood, Colin, Emma, Jason, Josh,

Housekeeping Pre-Meeting - 2pm Start

  1. Matters Arising (<10 mins)

    • Chris: handle SVS as discussed with Will.
    • Will: try Ice 3.4 for next week. PR Merged, and e-mail sent to devel
    • Emma: Potential Interview Dates to be circulated DONE
    • Emma: Gather info about WT site visit (Jan 10th) poster DONE
  2. Email and Forum Review - checked at (5 mins)

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

  2. Sprint Status

  3. Glencoe Update

  4. Minigroup Updates

    • HIC
    • Model
    • Web
    • FS
    • Usability
    • Paul Felts' pathology teaching resource
  5. Satellite Update

  6. Hackathon report (5 mins)

  7. Bio-Formats resources (5 mins)

    • Drupal, anyone?
  8. Any other business (<5 mins)

    • WT site visit 10th Jan


  • Josh (notes), Jean-Marie (notes), Will, Colin, Emma, Elwood (notes), Jason, Melissa (14:13), Mark (14:30), Curtis (14:50)

Housekeeping Pre-Meeting - 2pm Start

  1. Matters Arising (<10 mins)

  2. Chris: handle SVS as discussed with Will. PENDING

  3. Will: try Ice 3.4 for next week. PR Merged, and e-mail sent to devel

  4. Emma: Potential Interview Dates to be circulated DONE

  5. Emma: Gather info about WT site visit (Jan 10th) poster DONE

  6. Email and Forum Review - checked at (5 mins)

  7. Email - Two emails from Harri still to answer Josh to answer

  8. Forums -

  9. QA - various from Alexia link DONE

  10. Done at 14:12

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • OK
  2. Sprint Status

    • Jean-Marie: backlog stories at the start of each sprint

    • on per component (web, server, insight, etc.) created every sprint.

    • goal is to have those tasks completed per sprint to close story

    • web story had to be pushed to sprint5

      • idea is not to carry stories from sprint to sprint
      • create a branch related to that story.
      • Colin: one story for me. Was in sprint4, but re-evaluated it in sprint5
    • Josh: Ice 3.4 branch merged in along with others.

      • be aware of Ice 3.4 change for everyone (Josh sent e-mail to ome-devel 19/12)
    • Jason: Agilo broken whiteboard license expired.

  3. Glencoe Update

    • Jason: progress with hiring
    • sys admin starting in new year, Chris.
      • New developer in the pipeline, Oleg
      • Looking for Web designer. Jason, Josh to talk to potential candidate 21/12.
  4. Minigroup Updates

    • HIC: Elwood working on visual prototypes. Will be looking for feedback soon.
    • Model:
    • (EM meeting) * Invar sent a file related to EM (modelling) any discussion? * Will: not really, emails went round with feedback but their data model is more extensive than what we’re adding to ours * Jason: EMDB to be used as reference for the community, ‘make it happen’ from the community and they’ll give feedback. * Will: hdf as file format. “Wouldn’t it be great!” Still using mrc file format, key-value pairs.
    • J-M: Roi (hackathon) feedback * model very close to implementation e.g based on jhotdraw (for imageJ2) * Josh: Imglib - no strict 2D ROIs needs to support n-dim? * EMDB also discussed ROIs (“masks”) * Done 14:52
    • Web * Will: new look and feel template, header design, chat with j-m * maintain consistency with Insight, agreed on some things * J-M: can align a bit later when things have settled * Will: place things in same place in insight and web * J-M: presentation in new year to get feedback and discuss * Jason: what needs to be consistent and where can that be relaxed. * J-M: get the same experience and workflow within insight and web * Will: disk usage is based on pixels,bit depth and work out size * Doesn’t work with pyramids, fs, etc.
    • FS * Colin: Chris & Colin working on tweaking import paths, etc. * Pyramid files not catered for * Josh needs to be involved with public repos refactor * J-M: performance testing of new FS, on file formats * Colin: fails on some file formats (pyramid related), Chris wants to get SVS sorted
    • Usability * JM : Scott preseting at ImageJ2 * Hackathon report: comment that we should collect information about documentation and training material for Fiji, (client desktop applications) etc * cF., * communicate over documentation on github pages, will see how it progresses * Jason: could possibly reduce re-implementation efforts * Curtis: But it is more than that—it is a promise that those tools are striving to interoperate, work well together and avoid duplication of effort.
    • Paul Felts' pathology teaching resource * Will: notes are on email ticket (6166) * Couple of bugs in web that need verification and minor improvements * Happy with status of web and insight. Ready for next phase. * Jason: pathology to undergrads and medical students, want a way for them to access images with annotations, big images, real SVS files * Will: complex permissions stuff not necessary, simplifies things * LDAP questions, should be able to use UoD ldap not lifesci, should be groups related to Pauls groups. If not they can be set up easily enough * Will: images over a certain size are not viewable because XxY is bigger than integer value. Not in develop yet, in a branch, will require testing, not [production ready yet. Usually the biggest of 7 images some details we don’t see if they are not rendered. * Will: data on disk not an issue, hopefully up by 16th Jan (next semester) * J-M: friend in St. Andrews might be interested * Emma: Biochemists? (not medics/dentists) first group of students is a trial. * Jason: Action write to Chris. system req, ram, cpu, disk
  5. Satellite Update

    • Emma: have ad on redeployment for NIH position who will liaise with Ilya et al.
    • Jean-Marie: code style unified across Java, will was going to look at python code style.
    • Josh: try and apply style across entire code base.
    • Josh: CMU still having problems, needing features. Nothing from anyone else, very quiet. Time to be more involved?
    • J-M: Contacting Donald and Iain (Imperial)
    • Emma: Dates for next meeting, not much response yet. More of a hackathon style this time around.
    • J-M: Knime guys are willing to come back in Feb.
    • Jason: Contacting Bob Murphy at beginning of year to arrange a time to talk
    • Josh: Too slow for reading tables, opening/closing files
  6. Hackathon report (5 mins)

    • J-M: productive and good to have everyone from different projects together.
  7. Connected imagej2 and insight together.

  8. Curtis: ij2 plugins in insight. Cool.

    • J-M: java version support, IJ2 plugins using 1.5/6
      • Curtis: didn’t have time to try retrotranslation
      • Good discussion with Knime guys. (Tickets not yet created)
      • Plan is to have a proof-of-concept of workflow/interaction
    • Josh: J-M had a good idea :) insight works as blitz gateway. showed it to knime, happy with idea.
      • distribute insight as our gateway
      • Curtis, server version mismatch, Josh try and implement in the future
      • older servers 4.3 / 4.4 would be required to install an adapter to act like the new server
    • J-M: Icy - server vs client version is a blocker
    • Josh: block diagram of libraries to get them in same place, scifio will be used for file access
      • builds need to be sensible
      • imglib and imagej2 coming to 2.0 this year
    • Josh: webstart implemented, still needs J-M parameters discussion
    • Curtis: wondering about icy team if they chatted more about how to make the versioning happen
      • J-M: didn’t suggest anything in particular
    • J-M: will contact Fabrice about Icy-headless (mentioned at hackathon)
    • Curtis:
      • scijava is a great outcome
      • Need to keep pushing that forward.
      • imagej team will definitely be involved.
      • Unfortunate to not have a finished beta (there was more going out, etc.)
      • Updated all of the webresources
    • Melissa: Decent progress on getting us away from netcdf.
    • Jean-Marie: played badminton. Good idea.
    • Done 15:32 UK
  9. Bio-Formats resources (5 mins)

  10. Drupal, anyone?

  11. Josh: need content before we can review it

    • Curtis: will give a dump of bioformats site
    • Jason: help from lifesci dep with drupal?
  12. Any other business (<5 mins)

    • WT site visit 10th Jan
      • Jason: no meeting on 27th dec or 3rd dec
      • 10th is the Wellcome trust site visit, some team members will be involved in poster session but should be over by meeting time
      • Can do something Ad-hoc if needed before
    • Sprint 6: 3rd-18th bug fix effort! Get rid of major/critical (no blocker at the moment) tackle minor if we have time, did not go under 100 mark, now at 130.
      • Josh has rebased his change group branch and Josh & J-M to start work on it.
      • No timeline on 4.4 (across minigroups agree on when it can be delivered) estimate a date for delivery to freeze and start testing etc.
    • Done: 15:42 UK


* Chris: handle SVS as discussed with Will.
* Chris: request new agilo-pro license (expired)
* Will: schedule a brief talk in the new year about new web UI.
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