[ImageJ-devel] BioImaging ROI Spec

Thu Oct 11 08:13:17 CDT 2012

Hi all,

thanks for moving on with the topic.  I would love to join a hackathon
in Dundee, however, Nov 12-14 would not work for me.  Dec 10-12 is fine.

Best regards,
Stephan

On Thu, 2012-10-11 at 14:23 +0200, Tobias Pietzsch wrote: 
> Hi All,
> 
> Of course I would like to participate in this Hackathon.
> Dundee is fine with me and at the moment I would be free for both of the 
> proposed dates Nov 12-14 and Dec 10-12.
> 
> best regards,
> Tobias
> 
> On 10/11/2012 11:14 AM, tomancak wrote:
> > Hi Jason,
> >
> > Sorry that this comes rather late. I have been swamped with many
> > unrelated activities and this email thread is arguably long ;-).
> >
> > The discussion on ROIs started in Barcelona was a good one. This is
> > clearly a crucial feature to allow interoperability between our various
> > platforms. By sitting as a passive observer on the day long discussion,
> > I had a feeling that it is highly technical and I personally cannot
> > contribute much to it. It needs the people in the know to sit down
> > together and hammer it out. Thus a hackathon on this topic is indeed a
> > good idea, the 'politics' of this has been worked out at the various
> > meetings, it now needs someone who can actually do it.
> >
> > I will support the participation of Tobias and/or Stephan. Dundee is a
> > great location, we cannot do it in Dresden this time. I vote for Dundee.
> >
> > As for times, Stephan and Tobias will need to say when they could
> > participate. They have a lot on their plate, I cc'ed them explicitly to
> > my response so that they can speak up on this issue.
> >
> > Thanks for supporting and organizing this.
> >
> > All the best
> >
> > PAvel
> >
> > P.S. Sorry for top posting. The top posting Nazi is with me…. You know
> > who I mean </sarcasm>.
> >
> > -----------------------------------------------------------------------------------
> > Pavel Tomancak, Ph.D.
> >
> > Group Leader
> > Max Planck Institute of Molecular Cell Biology and Genetics
> > Pfotenhauerstr. 108
> > D-01307 DresdenTel.: +49 351 210 2670
> > GermanyFax: +49 351 210 2020
> >
> > email: tomancak at mpi-cbg.de <mailto:tomancak at mpi-cbg.de>
> > url : http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
> > twitter : http://twitter.com/PavelTomancak
> > <https://twitter.com/PavelTomancak>
> > -----------------------------------------------------------------------------------
> >
> >
> >
> > On Oct 8, 2012, at 5:15 PM, Jason Swedlow wrote:
> >
> >> Dear All-
> >>
> >> I'm writing following various discussions  regarding the definition
> >> and use of a common specification for multi-dimensional regions for
> >> biological imaging, and in particular biological microscopy.  I am
> >> cc'ing Michael Unser, Wiro Niessen and Antje Keppler on this email for
> >> reasons that I will describe below.  I've also included representation
> >> from OME, ImageJDev, KNIME, Icy, and CellProfiler.
> >>
> >> The first concrete discussion on a common ROI spec was held in April
> >> in Barcelona.  Josh Moore's notes were circulated earlier (also, see
> >> below).
> >>
> >> We now have an opportunity to finish this specification.  This follows
> >> from meetings sponsored by Euro-BioImaging (http://eurobioimaging.eu),
> >> and in particular The Data Management Work Package (often referred to
> >> as "WP11"), led by Wiro and Michael, and which I, through our work on
> >> OME, contribute to.  Through WP11, we have funds to sponsor a meeting
> >> that moves a common ROI spec towards completion.  The idea is to have
> >> a common specification, and example "proof-of-concept" software
> >> implementation(s) in at least a few of our projects, so that a region
> >> defined in one image software package can be used by another.  The
> >> emphasis is on transport and interop, and not, for example, on a
> >> single library for defining, using ROIs that must be used by all.  We
> >> already know the kind and level of standardization that works, and
> >> that which does not.
> >>
> >> Given the progress we made in Barcelona, it seems that this is not a
> >> fantasy, but an achievable goal.  We don't propose a standard meeting
> >> with presentations, etc., but more of a developer meeting or
> >> "hackathon", that has been so successfully used by the ImageJ/Fiji
> >> teams and others.  We need to work through the specification (ideally
> >> making some progress beforehand using the various electronic tools we
> >> all know and love), and then get at least rough implementations in place.
> >>
> >> As a start, we've used thescijava.org <http://scijava.org>site that
> >> was defined at the Dresden ImageJ/Fiji hackathon in Dec 2011.  See:
> >>
> >> http://www.scijava.org/
> >>
> >> As this was where our projects agreed to work together at the Dresden
> >> hackathon, it seemed a place where we could do this work, but this is
> >> not at all mandatory— just a place to start.  Whatever we use, it has
> >> to be usable for modern code development (in my opinion, that means,
> >> it has to be github or better, but other opinions welcome).  Obviously
> >> other resources can link to this.
> >>
> >> Below “Resources”, there is now a link to:
> >>
> >> http://www.scijava.org/roi-model/
> >>
> >> On this page are Josh Moore's notes from the Barcelona mtg.  With Lee
> >> Kamentsky's permission we can add his SpaceROI.xsd (email from 30
> >> April), or a more recent update to it.  Roger Leigh (OME) has added
> >> his work on a draft model spec.  He can explain what is going on there.
> >>
> >> For the mtg itself, we propose two possible dates— Nov 12-14 or Dec
> >> 10-12.  There are obviously several looming conflicts— US
> >> Thanksgiving, ASCB in SF, and several others.  I believe there is also
> >> an ImageJ hackathon looming.  So far there is strong preference for
> >> the November date.  Obviously minimising trans-ocean flights helps
> >> productivity and keeps us all in good graces with our families.  Wilma
> >> Woudenberg will send out a poll and we can try to get this nailed
> >> down.  If those dates don't work, we can go sooner or later, so speak
> >> up, but would be great to get this done before end of 2012.
> >>
> >> For location, we've discussed Dresden, Dundee, and there may be
> >> others.  Through Euro-BioImaging, Dundee has funds to sponsor the
> >> meeting, and to support travel for participants (economy only).  If
> >> possible, Dundee will do all travel arrangements, to save the fun of
> >> travel reimbursements from EU grants.
> >>
> >> I wasn't exactly sure who was interested, and we don't yet have a
> >> single mailing list that covers all of us, although the SciJava google
> >> group (https://groups.google.com/forum/?fromgroups#!forum/scijava) has
> >> been used for some  discussions.    This problem will get worse when
> >> we need our various developers to talk to each other.  I know many of
> >> the OME devs read the ImageJdev list, but that is not universal.  Note
> >> that some of the email lists included require registration, so do we
> >> use scijava at googlegroups?
> >>
> >> Ok, this a too long email.  Decisions needed:
> >>
> >> -- do we agree to use scijava to start this discussion?
> >> -- can we put materials, discussions we each have there?
> >> -- date for meeting—is there another scheduled event we should
> >> piggyback on? (Note I think things like the ImageJ mtg are not a good
> >> idea; too many other things going on)
> >> -- everyone OK with Dundee for mtg place??
> >>
> >> Note: I'm partial to Dundee, since we have to pay for everything, so
> >> it saves admin hassle, but if this can be solved easily, then that's
> >> fine.  Wilma will take care of Doodle polls and very likely travel.
> >>
> >> We've worked together well in the past, so hopefully we can get this
> >> done, and build something that will truly help our scientist users.
> >>
> >> Cheers,
> >>
> >> Jason
> >>
> >> P.S. As Euro-BioImaging will sponsor meeting, the various leaders of
> >> WP11 and also Antje Keppler, Euro-BioImaging PM are cc'd.
> >>
> >> **************************
> >> Wellcome Trust Centre for Gene Regulation & Expression
> >> College of Life Sciences
> >> MSI/WTB/JBC Complex
> >> University of Dundee
> >> Dow Street
> >> Dundee  DD1 5EH
> >> United Kingdom
> >>
> >> phone (01382) 385819
> >> Intl phone:  44 1382 385819
> >> FAX   (01382) 388072
> >> email:j.swedlow at dundee.ac.uk <mailto:j.swedlow at dundee.ac.uk>
> >>
> >> Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
> >> Open Microscopy Environment:http://openmicroscopy.org
> >> **************************
> >>
> >>
> >> The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> 