2011-12-20 Tuesday Meeting
Attending: Jean-Marie, Will, Elwood, Colin, Emma, Jason, Josh,
Housekeeping Pre-Meeting - 2pm Start
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
Email and Forum Review - checked at (5 mins)
Forums -
- alexc: Display Cellomics Image
- Code forum review
- Nov 29th Insight fails to retrieve thumbnails using 4.3.3
QA - various from Alexia link DONE
Agenda - 2:30pm Start
Accepting minutes from last meeting
Sprint Status
Glencoe Update
Minigroup Updates
- HIC
- Model
- Web
- FS
- Usability
- Paul Felts' pathology teaching resource
Satellite Update
Hackathon report (5 mins)
Bio-Formats resources (5 mins)
- Drupal, anyone?
Any other business (<5 mins)
- WT site visit 10th Jan
Attending
- 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
Matters Arising (<10 mins)
Chris: handle SVS as discussed with Will. PENDING
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
Email and Forum Review - checked at (5 mins)
Email - Two emails from Harri still to answer Josh to answer
Forums -
- alexc: Display Cellomics Image Melissa to answer
- Code forum review
- Nov 29th Insight fails to retrieve thumbnails using 4.3.3 Jean-Marie to answer
QA - various from Alexia link DONE
Done at 14:12
Agenda - 2:30pm Start
Accepting minutes from last meeting
- OK
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.
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.
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. github.com/scijava, http://scijava.github.com/ * 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
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
Hackathon report (5 mins)
- J-M: productive and good to have everyone from different projects together.
Connected imagej2 and insight together.
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 http://developer.imagej.net
- Melissa: Decent progress on getting us away from netcdf.
- Jean-Marie: played badminton. Good idea.
- Done 15:32 UK
-
J-M: java version support, IJ2 plugins using 1.5/6
Bio-Formats resources (5 mins)
Drupal, anyone? http://trac.openmicroscopy.org.uk/ome/ticket/7313
Josh: need content before we can review it
- Curtis: will give a dump of bioformats site
- Jason: help from lifesci dep with drupal?
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
-
WT site visit 10th Jan
Actions
* 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.