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<div class="moz-cite-prefix">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.<br>
<br>
--Lee<br>
<br>
On 10/8/2012 11:15 AM, Jason Swedlow wrote:<br>
</div>
<blockquote cite="mid:CC989962.15809%25j.r.swedlow@dundee.ac.uk"
type="cite">
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<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">Dear All-</span></p>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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).</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">We now have an opportunity
to finish this specification. This follows from meetings
sponsored by Euro-BioImaging (<a moz-do-not-send="true"
href="http://eurobioimaging.eu">http://eurobioimaging.eu</a>),
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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">As a start, we've used the
scijava.org site that was defined at the Dresden
ImageJ/Fiji hackathon in Dec 2011. See:</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"><a moz-do-not-send="true"
href="http://www.scijava.org">http://www.scijava.org</a>/</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.
</span></p>
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">Below “Resources”, there is
now a link to:</span></p>
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"><a moz-do-not-send="true"
href="http://www.scijava.org/roi-model/">http://www.scijava.org/roi-model/</a></span></p>
</div>
<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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 (<a moz-do-not-send="true"
href="https://groups.google.com/forum/?fromgroups#%21forum/scijava">https://groups.google.com/forum/?fromgroups#!forum/scijava</a></span>)
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@googlegroups?</p>
<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">Ok, this a too long email.
Decisions needed:</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">-- do we agree to use
scijava to start this discussion</span>?</p>
<p class="MsoNormal" style="font-family:Arial,sans-serif;
font-size:12px">-- can we put materials, discussions we each
have there?</p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">-- 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)</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">-- everyone OK with Dundee
for mtg place??</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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. </span></p>
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">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.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">Cheers,</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">Jason</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif">P.S. As Euro-BioImaging will
sponsor meeting, the various leaders of WP11 and also
Antje Keppler, Euro-BioImaging PM are cc'd.</span></p>
</div>
<div style="font-family:Arial,sans-serif; font-size:12px">
<p class="MsoNormal"><span style="font-size:9pt; color:black;
font-family:Arial,sans-serif"> </span></p>
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<div style="font-family:Arial,sans-serif; font-size:12px">
<div>
<div>
<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
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<p class="MsoNormal"><span style="font-size:9pt;
color:black; font-family:Arial,sans-serif">Wellcome
Trust Centre for Gene Regulation & Expression</span><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif"></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9pt;
color:black; font-family:Arial,sans-serif">College
of Life Sciences</span><span style="font-size:9pt;
color:black; font-family:Helvetica,sans-serif"></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;
color:black; font-family:Arial,sans-serif">MSI/WTB/JBC
Complex</span><span style="font-size:9pt;
color:black; font-family:Helvetica,sans-serif"></span></p>
</div>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">University of
Dundee</span></span><span style="font-size:9pt;
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style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">Dundee DD1 5EH</span></span><span
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font-family:Helvetica,sans-serif"></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">phone (01382)
385819</span></span><span style="font-size:9pt;
color:black; font-family:Helvetica,sans-serif"></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">Intl phone: 44
1382 385819 </span></span><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif"></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">FAX (01382)
388072 </span></span><span style="font-size:9pt;
color:black; font-family:Helvetica,sans-serif"></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">email:
<a moz-do-not-send="true"
href="mailto:j.swedlow@dundee.ac.uk">j.swedlow@dundee.ac.uk</a></span></span><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif"></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;
color:black; font-family:Helvetica,sans-serif"> </span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">Lab Page: </span></span><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif"><a
moz-do-not-send="true"
href="http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow">http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow</a></span></p>
</div>
<div>
<p class="MsoNormal"><span class="apple-style-span"><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif">Open Microscopy
Environment:
<a moz-do-not-send="true"
href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></span><span
style="font-size:9pt; color:black;
font-family:Helvetica,sans-serif"></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:9pt;
color:black; font-family:Helvetica,sans-serif">**************************</span></p>
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color:black; font-family:Helvetica,sans-serif"> </span></p>
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color:black; font-family:Helvetica,sans-serif"> </span></p>
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<br>
The University of Dundee is a registered Scottish Charity, No:
SC015096
</blockquote>
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