[ImageJ-devel] BioImaging ROI Spec

Tue Oct 9 01:37:57 CDT 2012

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 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.
>  
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__________________________________________________________.
Michael Unser, Professor
Biomedical Imaging Group
Ecole Polytechnique Fédérale de Lausanne

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