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Hi Will,<br>
<br>
Thanks very much for this very decent partial fix. Indeed, this now
works for me. There is still the issue noted in the TODO note but it
now completes the metadata population for my 20 by 35 arrays without
errors and I can go on with my work.<br>
<br>
This is great!<br>
- Damir<br>
<br>
<div class="moz-cite-prefix">On 7/4/2016 5:16 AM, William Moore
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:B428F95E-861D-41B2-99EE-10E5563DAEF1@dundee.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Damir,
<div class=""><br class="">
</div>
<div class="">(Apologies if you get duplicates of this message -
been updating my ome-devel settings)</div>
<div class="">(PR opened at I’ve opened a PR with this fix at <a
moz-do-not-send="true"
href="https://github.com/openmicroscopy/openmicroscopy/pull/4743"
class=""><a class="moz-txt-link-freetext" href="https://github.com/openmicroscopy/openmicroscopy/pull/4743">https://github.com/openmicroscopy/openmicroscopy/pull/4743</a></a>)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""> How do you want to name your Wells in the csv
file?</div>
<div class="">If you name Wells like</div>
<div class=""><br class="">
</div>
<div class="">…</div>
<div class="">Z01</div>
<div class="">AA01</div>
<div class="">AA02</div>
<div class="">etc.</div>
<div class=""><br class="">
</div>
<div class="">then you can add these lines to
populate_metadata.py to extend the AS_ALPHA by another 26
rows.</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-family: Courier; color: rgb(76,
47, 45); background-color: rgb(223, 219, 196);" class="">
AS_ALPHA = [chr(v) for v in range(97, 122 + 1)] # a-z</div>
<div style="margin: 0px; font-family: Courier; color: rgb(0,
165, 0); background-color: rgb(223, 219, 196);" class="">
+ # Support more than 26 rows</div>
<div style="margin: 0px; font-family: Courier; color: rgb(0,
165, 0); background-color: rgb(223, 219, 196);" class="">
+ for v in range(97, 122 + 1):</div>
<div style="margin: 0px; font-family: Courier; color: rgb(0,
165, 0); background-color: rgb(223, 219, 196);" class="">
+ AS_ALPHA.append('a' + chr(v))</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76,
47, 45); background-color: rgb(223, 219, 196);" class="">
WELL_REGEX = re.compile(r'^([a-zA-Z]+)(\d+)$’)</div>
</div>
<div class=""><br class="">
</div>
<div class="">This works for me with my local setup.</div>
<div class=""><br class="">
</div>
<div class="">I haven’t discussed with the Glencoe authors of
the script whether this is the “right” way to fix this, but</div>
<div class="">please let us know if it works for you?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> Cheers,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 3 Jul 2016, at 01:15, Damir Sudar <<a
moz-do-not-send="true" href="mailto:dsudar@lbl.gov"
class=""><a class="moz-txt-link-abbreviated" href="mailto:dsudar@lbl.gov">dsudar@lbl.gov</a></a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">Hi
Eleanor and OME team,<br class="">
<br class="">
When trying to use the various metadata populate
utilities for our project I ran into what I think is a
bug:<br class="">
<br class="">
When the number of rows in a plate exceeds 26 (i.e.
beyond row "Z"), the Populate_Metadata.py script (and
presumably the underlying functionality that does the
actual work) fails with the error:<br class="">
<blockquote type="cite" class="">
<pre class="">Traceback (most recent call last):
File "./script", line 130, in <module>
message = populate_metadata(client, conn, scriptParams)
File "./script", line 85, in populate_metadata
ctx = ParsingContext(client, omero_object, "")
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 442, in __init__
self.value_resolver = ValueResolver(self.client, self.target_object)
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 245, in __init__
return self.load_plate()
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 318, in load_plate
self.target_object, wells_by_location, wells_by_id, images_by_id
File "/home/omero_user/OMERO.server/lib/python/omero/util/populate_metadata.py", line 330, in parse_plate
columns = wells_by_location[self.AS_ALPHA[row]]
IndexError: list index out of range</pre>
</blockquote>
<br class="">
I'm working with high density printed microarray grids
of 20 by 35 cell-spots in 8-well plates and I'm
abusing the the Screen/Plate/Well functionality by
treating each cell spot as a Well, each Array as a
Plate, and each of my 8-well plates as a Screen. So
far all this works great until this point.<br class="">
<br class="">
I tried some work-arounds such as changing the naming
scheme of Rows and Columns (as Dataset_To_Plate.py
allows) so that the Rows get the numbers and the
Columns get the letters but alas, that fails with the
same error so the max number of rows limit of 26
appears to be pretty deeply embedded somewhere.<br
class="">
<br class="">
So I looked at the piece of code
(populate_metadata.py) where this fails and found two
issues:<br class="">
1) the TODO note: which explains why my work-around
failed<br class="">
<blockquote type="cite" class=""> # TODO: This
should use the PlateNamingConvention. We're assuming
rows<br class="">
# as alpha and columns as numeric.<br
class="">
</blockquote>
2) the AS_ALPHA macro evaluates incorrectly when the
row is interpreted as a single letter: which is why
anything past "Z" fails<br class="">
<br class="">
Any chance someone smarter than I could have a look
and fix?<br class="">
<br class="">
Thanks,<br class="">
- Damir<br class="">
<br class="">
<br class="">
<div class="moz-cite-prefix">On 6/27/2016 2:03 PM,
Eleanor Williams wrote:<br class="">
</div>
<blockquote
cite="mid:5439e213-8039-e3f4-0b51-84077dd915d1@dundee.ac.uk"
type="cite" class="">
<p class="">Hi Damir</p>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">To
convert the omero tables to key-value pairs
annotations we are again using the CLI metadata
populate script along with a yaml-format
configuration file to specify which columns we
want to take from the omero tables and put into
Key-Value Annotations.
<br class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""><br
class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">This
component of the metadata functionality is still
in the development stage and so to use it you
need to:</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""><br
class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">1. use
the latest version of omero (5.2.4) and</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">2.
then run as</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">OMERO_DEV_PLUGINS=1
bin/omero metadata populate --context bulkmap
--cfg bulkmap-config.yml Screen:n</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">where
n is the screen number in omero.</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""><br
class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">An
example config file for one of our screens is
here</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><a
moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml"
style="text-decoration:none;" class=""><span
style="font-size:14.666666666666666px;font-family:Arial;color:#1155cc;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;"
class=""></span></a><a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml">https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml</a></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""><br
class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">You
can see I have just picked out some of the
columns from the</span><a moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-annotation.csv"
style="text-decoration:none;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""></span><span
style="font-size:14.666666666666666px;font-family:Arial;color:#1155cc;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;"
class="">annotation.csv</span></a><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""> file,
in this case ones that I thought IDR users might
use as search terms, and I have specified URLs
for some. You can also change the 'display
name' of the column using the ' clientname' tag
and create URLs using the 'clientvalue' tag. </span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class=""><br
class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class=""><span
style="font-size: 14.666666666666666px;
font-family: Arial; background-color:
transparent; font-weight: 400; font-style:
normal; font-variant: normal; text-decoration:
none; vertical-align: baseline;" class="">Let us
know if you have any problems running this, or
suggestions for improvement.</span></div>
Best regards<br class="">
Eleanor<br class="">
<br class="">
<div class="moz-cite-prefix">On 27/06/2016 03:04,
Damir Sudar wrote:<br class="">
</div>
<blockquote
cite="mid:e00055fc-3c7b-acf4-30fa-3d6061190286@lbl.gov"
type="cite" class="">
Hi Eleanor and Josh,<br class="">
<br class="">
I'm learning a lot from your work on putting the
IDR together and I'm applying it for our image
repository for our LINCS project (<a
moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.lincsproject.org/centers/data-and-signature-generating-centers/oregon-u/"><a class="moz-txt-link-freetext" href="http://www.lincsproject.org/centers/data-and-signature-generating-centers/oregon-u/">http://www.lincsproject.org/centers/data-and-signature-generating-centers/oregon-u/</a></a>)
that hopefully will go live in a few months. We're
also looking at Zegami as a possible way to
provide visualizations of that data (Great demo,
Roger!! and thanks for the code for that).<br
class="">
<br class="">
I've gotten as far as putting my metadata into a a
format that can be used to generate the omero
tables using the Populate Metadata script. But I
couldn't find how you guys then populate the
Key-Value Annotations. It appears to be a subset
of what's in the Tables. Do you have some magic
scripts for that and are those available?<br
class="">
<br class="">
Cheers,<br class="">
- Damir<br class="">
<br class="">
<div class="moz-cite-prefix">On 6/16/2016 2:21 AM,
Eleanor Williams wrote:<br class="">
</div>
<blockquote
cite="mid:bacc151b-5e5c-4af6-f31d-26a7559d457f@dundee.ac.uk"
type="cite" class="">
<p class="">Hi Steve and Roger<br class="">
</p>
<p class="">I think idr0002-heriche-condensation
would be a good screen to start with. It is
relatively small at 12 plates and has good
annotation with control, quality control and
phenotype values. It can be found here
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://idr-demo.openmicroscopy.org/webclient/?show=screen-102">
http://idr-demo.openmicroscopy.org/webclient/?show=screen-102</a>.<br
class="">
</p>
<p class="">I am doing a bit of a stock-take of
the annotation files I've produced so far and
will be changing a few aspects over the next
few weeks, mainly to include more of the
information that is currently held in the
study files. For example I'd like to get more
of the sample attributes such as species and
cell line into the annotation.csv file, and
then into the omero tables and Map
Annotations. Sample attributes for screens
were originally recorded in the study file
because it didn't vary per screen, but now
that we are also looking at non-screen data
where this might vary it makes sense to always
have it visible with the images. Also we
haven't got as far as exposing much of the
study information in omero yet.
<br class="">
</p>
<p class="">I would really like to work with you
to understand how you are going to use the
experimental and analytic annotations and how
we can help in providing the metadata you need
and in the most usable format. For example
would it be useful if I indicate what is
sample attribute information in the
annotation.csv file by using something like a
constistent header format e.g. Characterisics
[Organism], Characteristics [Cell Line],
Characteristics [Organism Part] etc, or is
this not really necessary for your purposes
and 'Organism', 'Cell Line' column headings
would be enough? <br class="">
</p>
<p class="">Finally, it was <a
moz-do-not-send="true"
href="https://www.openmicroscopy.org/site/about/development-teams/jason/balaji.png/view"
class="">
Balaji Ramalingam</a> that you were talking
to about streaming the thumbnails. I'm sure
he would be happy to discuss this further with
you.
<br class="">
</p>
<p class="">Best regards</p>
<p class="">Eleanor</p>
<p class=""><br class="">
</p>
<p class=""><br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 15/06/2016
20:59, Josh Moore wrote:<br class="">
</div>
<blockquote
cite="mid:CAD3Ea=X2o+AewGgw0aCJGkaDfJbMDqsNZAHeC3QuHKSknHpiGQ@mail.gmail.com"
type="cite" class="">
<pre class="" wrap="">Forwarding this to the mailing list so that anyone who had expressed
interested in <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://zegami.com/">http://zegami.com/</a> at this year's users' meeting can
follow along.
Cheers,
~Josh
P.S. If you weren't able to attend #OME2016, a recap is now up on the
blog <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://blog.openmicroscopy.org/community/2016/06/15/user-meeting/">http://blog.openmicroscopy.org/community/2016/06/15/user-meeting/</a>
---------- Forwarded message ----------
From: Stephen Taylor <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a>
Date: Tue, Jun 14, 2016 at 8:17 AM
Subject: Re: [IDR Project] Zegami / IDR
Cc: Roger Noble <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:roger@zegami.com"><roger@zegami.com></a>
Hi,
I’ve been look at a few examples from the link Josh sent to me and
there are quite a lot! What would be a good data set to get import
into Zegami from IDR? I am thinking a set that has decent metadata
and a study that people are more familiar with that would make an
interesting use case.
Kind regards,
Steve
From: Stephen Taylor
Sent: 10 June 2016 14:25
Cc: Roger Noble <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:roger@zegami.com"><roger@zegami.com></a>; '<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:e.x.williams@dundee.ac.uk">e.x.williams@dundee.ac.uk</a>'
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:e.x.williams@dundee.ac.uk"><e.x.williams@dundee.ac.uk></a>
Subject: RE: [IDR Project] Zegami / IDR
Hi all,
I am interested generally in getting data in and out of OMERO from
both internal and external. Over a WAN the images are less of an issue
since they are streamed on demand but large metadata on the other hand
can get out of hand since it all has to be loaded completely into
Zegami’s database.
Currently I do “OMERO project” to “Zegami collection” using a Zegami
export script (modified version of the OMERO batch export script).
This takes a project or selection of images from OMERO and produces
thumbnails and data in tab delimited Zegami format and then I manually
import that into Zegami for processing. The OMERO id is preserved so I
can link to the original image in OMERO using the OMERO web client. I
only export certain metadata currently (filenames and OMERO tags) and
my plan is to make this more comprehensive and allow MapAnnotations
and Tables to be exported using this mechanism as well. I need to find
out more how to query these data types. Since we have internal
projects at Oxford that need this I’d like to finish this and make
that plugin freely available for other OMERO users to publish their
data in Zegami.
Longer term for IDR/Zegami
One of your team (apologies I didn’t get his name but he was doing
OMERO/ImageJ in the Unconference session) suggested we just stream in
the thumbnail and just have 1 level (i.e. no zoom) and when you want
to see the image just open it up in OMERO. This would not be as nice
to use but may be sufficient for HCS and would allow you to use
Zegami’s facet based query engine and would be probably little (no?)
work for you guys. We need to test this to see what it looks like and
it assumes OMERO can supply a unique thumbnail URL for each image and
that the metadata will provide a primary key so that we can get to
this image via a thumbnail id. To get at the metadata Josh and Eleanor
said they were thinking of making the CSV downloadable for a
collection, which could be loaded into Zegami on the fly (we have
instances where we dynamically load metadata via URL already).
However, major caveat is on how well this would perform over a WAN
with a large amount of data.
BTW we have developer docs for Zegami for those interested at:
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://support.zegami.com/hc/en-us/categories/200350657-Developers">https://support.zegami.com/hc/en-us/categories/200350657-Developers</a>
and would welcome feedback.
Kind regards and thanks,
Steve
From: Jason Swedlow (Staff) [<a moz-do-not-send="true" class="moz-txt-link-freetext" href="mailto:j.r.swedlow@dundee.ac.uk">mailto:j.r.swedlow@dundee.ac.uk</a>]
Sent: 08 June 2016 13:09
Cc: Eleanor Williams (Staff) <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:e.x.williams@dundee.ac.uk"><e.x.williams@dundee.ac.uk></a>
Subject: Re: [IDR Project] Zegami / IDR
Hi Josh et al—
My two cents— can we consider this use case from an external users’
perspective, mindful that distribution of such a solution would
definitely cause us to consider how we ship thumbnails, handle
straws, etc.
Cheers,
Jason
On Wed, Jun 8, 2016 at 1:31 PM, Josh Moore <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:josh@glencoesoftware.com"><josh@glencoesoftware.com></a> wrote:
Stephen,
On Wed, Jun 8, 2016 at 9:52 AM, Stephen Taylor
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a> wrote:
</pre>
<blockquote type="cite" class="">
<pre class="" wrap="">Hi Josh,
Yes! What would be the best way of bulk downloading the thumbnails for a screen or plate
</pre>
</blockquote>
<pre class="" wrap="">Interesting question. Guess the reverse question is: do you want to do
this as an external user or as if you had access to the OMERO?
</pre>
<blockquote type="cite" class="">
<pre class="" wrap="">( I notice the "Run Script" button isn't active ).
</pre>
</blockquote>
<pre class="" wrap="">Correct. This server is stripped down in several ways as a public resource.
~J.
</pre>
<blockquote type="cite" class="">
<pre class="" wrap="">Kind regards,
Steve
</pre>
</blockquote>
<pre class="" wrap="">-----Original Message-----
From: Josh Moore [<a moz-do-not-send="true" class="moz-txt-link-freetext" href="mailto:josh@glencoesoftware.com">mailto:josh@glencoesoftware.com</a>]
Sent: 08 June 2016 08:07
To: Stephen Taylor <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a>
Cc: Eleanor Williams <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:exwilliams@dundee.ac.uk"><exwilliams@dundee.ac.uk></a>;
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:e.x.williams@dundee.ac.uk">e.x.williams@dundee.ac.uk</a>; <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:j.a.moore@dundee.ac.uk">j.a.moore@dundee.ac.uk</a>
Subject: Re: Zegami / IDR
Hi Stephen,
On Wed, Jun 8, 2016 at 8:40 AM, Stephen Taylor
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a> wrote:
</pre>
<blockquote type="cite" class="">
<pre class="" wrap="">Hi Eleanor,
Thanks very useful. Is the web site publically available?
</pre>
</blockquote>
<pre class="" wrap="">You mean <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://idr-demo.openmicroscopy.org/webclient">http://idr-demo.openmicroscopy.org/webclient</a> ?
Cheers,
~Josh
</pre>
<blockquote type="cite" class="">
<pre class="" wrap="">Kind regards and thanks,
Steve
</pre>
</blockquote>
<blockquote type="cite" class="">
<pre class="" wrap="">From: Eleanor Williams [<a moz-do-not-send="true" class="moz-txt-link-freetext" href="mailto:exwilliams@dundee.ac.uk">mailto:exwilliams@dundee.ac.uk</a>]
Sent: 07 June 2016 11:09
To: Stephen Taylor <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a>;
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:e.x.williams@dundee.ac.uk">e.x.williams@dundee.ac.uk</a>; <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:j.a.moore@dundee.ac.uk">j.a.moore@dundee.ac.uk</a>
Subject: Re: Zegami / IDR
Hi Stephen
Here is a link to our workshop presentation but it describes how to
get the data into omero rather than out.
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://downloads.openmicroscopy.org/presentations/2016/Users-Meeting/Workshops/Metadata-at-Scale.pdf">http://downloads.openmicroscopy.org/presentations/2016/Users-Meeting/Workshops/Metadata-at-Scale.pdf</a>
We will be adding the annotation.csv files as attachments to each
screen over the next couple of weeks.
Let us know if you have any more questions.
Best regards
Eleanor
</pre>
</blockquote>
<blockquote type="cite" class="">
<pre class="" wrap="">On 07/06/2016 10:41, Stephen Taylor wrote:
Hi Eleanor and Josh,
Great to meet you both at the OME meeting last week.
I'd be interested in trying get some data into Zegami from IDR. I
missed your Unmeeting (ironically I was demoing Zegami) where I think
you went into some of the technical details. Can you send me the link
to your presentation please?
Kind regards and thanks,
Steve
</pre>
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<br class="">
<pre class="moz-signature" cols="72">--
Eleanor Williams PhD
Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK</pre>
<br class="">
<span style="font-size:10pt;" class="">The
University of Dundee is a registered Scottish
Charity, No: SC015096</span>
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<pre class="moz-signature" cols="72">--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
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Visiting Scientist, Oregon Health & Science University</pre>
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<br class="">
<pre class="moz-signature" cols="72">--
Eleanor Williams PhD
Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK</pre>
<br class="">
<span style="font-size:10pt;" class="">The
University of Dundee is a registered Scottish
Charity, No: SC015096</span>
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<br class="">
<pre class="moz-signature" cols="72">--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
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Visiting Scientist, Oregon Health & Science University</pre>
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<br>
<pre class="moz-signature" cols="72">--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
<a class="moz-txt-link-freetext" href="http://biosciences.lbl.gov/profiles/damir-sudar-2/">http://biosciences.lbl.gov/profiles/damir-sudar-2/</a>
Visiting Scientist, Oregon Health & Science University</pre>
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