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: [email protected] <mailto:[email protected]> > > 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@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:[email protected] <mailto:[email protected]> > >> > >> 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 > > > _______________________________________________ ImageJ-devel mailing list [email protected] http://imagej.net/mailman/listinfo/imagej-devel
