[ImageJ-devel] BioImaging ROI Spec

Thu Oct 11 07:23:31 CDT 2012

Hi All,

Of course I would like to participate in this Hackathon.
Dundee is fine with me and at the moment I would be free for both of the 
proposed dates Nov 12-14 and Dec 10-12.

best regards,
Tobias

On 10/11/2012 11:14 AM, tomancak wrote:
> 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 DresdenTel.: +49 351 210 2670
> GermanyFax: +49 351 210 2020
>
> email: tomancak at mpi-cbg.de <mailto:tomancak at mpi-cbg.de>
> url : http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
> twitter : http://twitter.com/PavelTomancak
> <https://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 thescijava.org <http://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 <mailto: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
>