[ImageJ-devel] BioImaging ROI Spec

[Jason Swedlow]

Dear All-

Thanks for your support, enthusiasm, and your patience on the arrangements on this meeting.  There have been alot of people to track.  Finally, here are the details:


1.       First meeting will be Nov 12-14 in Dundee.  We'll start first thing in the morning on the 2th, so plan on arriving Nov 11, or Nov 10 if necessary.  As most, but not all people could attend then, we'll schedule a follow-on remote meeting (using VoIP, shared screens etc.) in December, to follow up on any issues.  We have access to Webex, Adobe Connect and Jabber, IRC and others.  We can decide how we want to run that later, based on what we need.

2.       Wilma Woudenberg will make all travel arrangements for the November meeting.  She'll be in touch soon with more info.  Please do respond to any queries from Wilma  for details as soon as you can.

3.       All funding will be from Euro-BioImaging WP11 meeting funds.

4.       Current proposal is to use the scijava resources for all pre-meeting discussion and code sharing.  See:

https://groups.google.com/forum/?fromgroups#!forum/scijava

and

 https://github.com/scijava/roi-model

This is not proscriptive- we just want something that works and is open and available.  Scijava is there, in use, and until it breaks seems the right thing to use.

5.       Most important will be review and consideration of docs and other resources that appear on scijava BEFORE the meeting, so that everyone comes ready to work.

6.       We will write a report on the output of these efforts, and include that in various reports that are part of Euro-BioImaging.  This report will summarise the problem, the activity, and reference the outputs in docs and software.  All participants and PIs will be listed as authors.  We can decide whether that should also be published separately later.

Just so we are clear, this is NOT a PI meeting (with lots of high level talks, PPTs, and people doing their emails), but work focussed on the technical details and implementation of a common ROI specification for our domain of bioimaging.

>From here on out, all discussion and arrangements will appear on scijava.

Thanks again.  See you in a few weeks.

Cheers,

Jason

P.S. Am sending identical email to CellProfiler, KNIME and Icy teams.  They are separate because otherwise they get blocked as spam (too many addresses).


From: Jason Swedlow
Sent: Friday, October 12, 2012 11:55 AM
To: Stephan Preibisch; OME Nitpick; imagej-devel at imagej.net
Cc: Lee Kamentsky; Christian Dietz; Martin Horn; chaumont at pasteur.fr; Jean-Christophe Olivo-Marin; Wilma Woudenberg; Michael Unser; EUBIdundee; Anne Carpenter; tomancak at mpi-cbg.de; Antje Keppler; w.niessen at erasmusmc.nl; Michael Berthold
Subject: Re: [ImageJ-devel] BioImaging ROI Spec

Dear All-

Thanks very much for the responses, and the interest and commitment to this effort.  Yes, it's boring infrastructure, but it's also important and will deliver value to our scientists users.

Let me do some schedule checking and then get back to you all on final dates.  Will be in touch soon.

Cheers,

Jason

**************************
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
**************************



From: Stephan Preibisch <preibischs at janelia.hhmi.org<mailto:preibischs at janelia.hhmi.org>>
Date: Thursday, 11 October 2012 18:30
To: Jason Swedlow <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>>
Cc: OME Nitpick <ome-nitpick at lists.openmicroscopy.org.uk<mailto:ome-nitpick at lists.openmicroscopy.org.uk>>, "imagej-devel at imagej.net<mailto:imagej-devel at imagej.net>" <imagej-devel at imagej.net<mailto:imagej-devel at imagej.net>>, Lee Kamentsky <leek at broadinstitute.org<mailto:leek at broadinstitute.org>>, Christian Dietz <christian.dietz at uni-konstanz.de<mailto:christian.dietz at uni-konstanz.de>>, Martin Horn <martin.horn at uni-konstanz.de<mailto:martin.horn at uni-konstanz.de>>, "chaumont at pasteur.fr<mailto:chaumont at pasteur.fr>" <chaumont at pasteur.fr<mailto:chaumont at pasteur.fr>>, Jean-Christophe Olivo-Marin <jcolivo at pasteur.fr<mailto:jcolivo at pasteur.fr>>, Wilma Woudenberg <W.Woudenberg at dundee.ac.uk<mailto:W.Woudenberg at dundee.ac.uk>>, Michael Unser <michael.unser at epfl.ch<mailto:michael.unser at epfl.ch>>, EUBIdundee <EUBIdundee at dundee.ac.uk<mailto:EUBIdundee at dundee.ac.uk>>, Anne Carpenter <anne at broadinstitute.org<mailto:anne at broadinstitute.org>>, "tomancak at mpi-cbg.de<mailto:tomancak at mpi-cbg.de>" <tomancak at mpi-cbg.de<mailto:tomancak at mpi-cbg.de>>, Antje Keppler <keppler at embl.de<mailto:keppler at embl.de>>, "w.niessen at erasmusmc.nl<mailto:w.niessen at erasmusmc.nl>" <w.niessen at erasmusmc.nl<mailto:w.niessen at erasmusmc.nl>>, Michael Berthold <Michael.Berthold at Uni-Konstanz.DE<mailto:Michael.Berthold at Uni-Konstanz.DE>>
Subject: Re: [ImageJ-devel] BioImaging ROI Spec

Hi everybody,

I would really like to participate as well. But I could unfortunately only make it 10-12 December.

Thanks a lot for organizing this Hackathon Jason!

Hope to see you soon,
Stephan

On Oct 8, 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<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
**************************



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