[ImageJ-devel] BioImaging ROI Spec

[Anne Carpenter]

Thanks for getting us organized, Jason.  I want to confirm that the
CellProfiler team is supportive and Lee will represent us.

And yes, we would be very happy to provide meeting space in Boston -
we would love to have the group here for future events.

Anne

Anne E. Carpenter, Ph.D.
Director, Imaging Platform
Broad Institute of Harvard and MIT
Five Cambridge Center, 1321
Cambridge MA 02142
anne at broadinstitute.org
phone: (617) 714-7750
http://www.broadinstitute.org/~anne


On Thu, Oct 11, 2012 at 9:37 AM, Lee Kamentsky <leek at broadinstitute.org> wrote:
> I'm pretty sure I'll go to the meeting - both sets of dates are OK for me.
> I'll check in again when the plans become final and make the necessary
> arrangements. I think it would be useful if we could have some sort of
> scratchpad or wiki to discuss the spec prior to going. I have one or two
> use-cases that are challenging and also I want to plan how to address
> scalability issues and possibly benchmark a couple of approaches on real
> data.
>
> --Lee
>
>
> On 10/8/2012 11:15 AM, 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.
>
>
>
> **************************
>
> 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: j.swedlow at dundee.ac.uk
>
>
>
> 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
>
>