[ImageJ-devel] BioImaging ROI Spec

Tue Oct 9 13:32:52 CDT 2012

Hi Jason,

Thanks for the thorough summary.

> -- do we agree to use scijava to start this discussion?

Yes, I agree that the scijava mailing list is the best place for further
discussion:
    https://groups.google.com/forum/?fromgroups#!forum/scijava

> -- can we put materials, discussions we each have there?

Indeed, though I think technical materials should go into the
@scijava/roi-model repository:
    https://github.com/scijava/roi-model

We can add anyone interested in contributing to the committers list. (Or
you can fork it and submit a PR; either way.)

Figuring out how to organize everything might be a bit tricky, though.

> -- 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)

Well, the ImageJ conference (Oct 24-26) is the only time I will be in the
EU otherwise. So no, there is no other meeting that would be convenient for
me personally to piggyback on.

> -- everyone OK with Dundee for mtg place??

Dundee is OK with me, as far as the EU goes. That said, I was recently
lamenting how (with respect to international flights) all of our groups are
based in smaller cities off the proverbial beaten path: Dundee, Dresden,
Madison, Konstanz... But Paris (Pasteur) & Boston (Broad/CellProfiler) are
also represented here! Maybe the big city folks want to organize one of
these shindigs in the future?

Regards,
Curtis

On Mon, Oct 8, 2012 at 10:15 AM, Jason Swedlow <j.r.swedlow at dundee.ac.uk>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.
>
>
>
> **************************
>
> Wellcome Trust Centre for Gene Regulation & Expression
>
> College of Life Sciences
>
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>
> University of Dundee
>
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>
> Dundee  DD1 5EH
>
> United Kingdom
>
>
>
> phone (01382) 385819
>
> Intl phone:  44 1382 385819
>
> FAX   (01382) 388072
>
> email: j.swedlow at dundee.ac.uk
>
>
>
> Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
>
> Open Microscopy Environment: http://openmicroscopy.org
>
> **************************
>
>
>
>
>
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>
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