Dear Jason: Thanks for this initiative. Ricard Delgado, who developed a very nice active contour segmentation software which relies a lot on ROI (cf. my talk at Bioimage informatics in Dresden), is ready to participate as a representative of my lab. He is available at the proposed date.
Best, -Michael On 8 oct. 2012, at 17:15, 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 __________________________________________________________. Michael Unser, Professor Biomedical Imaging Group Ecole Polytechnique Fédérale de Lausanne Mailing address: Prof. Michael Unser EPFL, LIB BM 4.136 (Batiment BM) Station 17 CH-1015 Lausanne Switzerland E-Mail: [email protected] URL : http://bigwww.epfl.ch/ Tel.: +41(21)693.51.75 Secr.: +41(21)693.11.85 Fax : +41(21)693.37.01 __________________________________________________________. _______________________________________________ ImageJ-devel mailing list [email protected] http://imagej.net/mailman/listinfo/imagej-devel
