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 Dresden Tel.: +49 351 210 2670 Germany Fax: +49 351 210 2020 email: [email protected] url : http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html twitter : http://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 the 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] > > 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
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