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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Eleanor,<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt">
<p style="margin-left:5.25pt">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 href="http://idr-demo.openmicroscopy.org/webclient/?show=screen-102">http://idr-demo.openmicroscopy.org/webclient/?show=screen-102</a>.<span style="color:#1F497D"><o:p></o:p></span></p>
</div>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">These look good. Thanks!<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p>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.
<o:p></o:p></p>
<p>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? <o:p></o:p></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Key information would be OMERO id of the thumbnail (to potentially stream) and OMERO id so we can link back to the full image in the OMERO database<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">So then we can construct URLs like this:<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><a href="http://idr-demo.openmicroscopy.org/webgateway/render_thumbnail/179717/96/">http://idr-demo.openmicroscopy.org/webgateway/render_thumbnail/179717/96/</a><o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><a href="http://idr-demo.openmicroscopy.org/webclient/img_detail/179715/">http://idr-demo.openmicroscopy.org/webclient/img_detail/179715/</a><o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Plate, Well id (or number) is also pretty useful. Do you think we would need to write a Plate Viewer to organise the tiles for the user?<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I would imagine in a lot of studies we won’t have control on how they are annotated. Zegami can read most data sources by writing an appropriate data loader plugin, so I think
the issue is how fast can we get the metadata out of OMERO and what level of caching would be required on the Zegami side. For example, if the data is in available as a single flat table (such as .csv/.tsv) format it should be feasible to load a collection
of this size dynamically (1152 wells) since I did something similar by reading a shared Google Spreadsheet. Very large metadata files will be a bigger problem.<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">With regards to other information needed I think it depends on the biological question. For example, this experiment is published so the analysis has been done and summary statistics
produced for each well (Quality Control, Median Deviation Fraction - Shorter Prophase, Median Deviation Fraction - Longer Prophase, Phenotype Reproducibility - Shorter Prophase etc) and these could all be imported in as a mixture of categorical and numeric
data and then sorted and filtered. i.e. show me all the wells where Quality Control is “pass” and then sort on “Median Deviation Fraction - Longer Prophase:”. The scientist then can review the images to identify candidate wells, then link to the time series
in OMERO to the well of interest. You could also feed in a whole bunch of other statistics to help verify the methods during development of the screen. For example, in this case the authors use CellCognition software to classify nuclei stages (interphase,
early prophase, late prophase, prometaphase, metaphase) and you could verify how well the algorithms are doing by having a %nuclei stage for each well. This would allow you to look for wells that had more cells in prometaphase for example and check the analysis
is correct. You could also add in various gene annotations, and other metadata that was useful.
<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p>Finally, it was <a href="https://www.openmicroscopy.org/site/about/development-teams/jason/balaji.png/view">
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.
<o:p></o:p></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Ok great.<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Please let me know if you have any further questions.<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Kind regards,<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Steve<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p>Best regards<o:p></o:p></p>
<p>Eleanor<o:p></o:p></p>
<p><o:p> </o:p></p>
<p><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 15/06/2016 20:59, Josh Moore wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Forwarding this to the mailing list so that anyone who had expressed<o:p></o:p></pre>
<pre>interested in <a href="http://zegami.com/">http://zegami.com/</a> at this year's users' meeting can<o:p></o:p></pre>
<pre>follow along.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers,<o:p></o:p></pre>
<pre>~Josh<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>P.S. If you weren't able to attend #OME2016, a recap is now up on the<o:p></o:p></pre>
<pre>blog <a href="http://blog.openmicroscopy.org/community/2016/06/15/user-meeting/">http://blog.openmicroscopy.org/community/2016/06/15/user-meeting/</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>---------- Forwarded message ----------<o:p></o:p></pre>
<pre>From: Stephen Taylor <a href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a><o:p></o:p></pre>
<pre>Date: Tue, Jun 14, 2016 at 8:17 AM<o:p></o:p></pre>
<pre>Subject: Re: [IDR Project] Zegami / IDR<o:p></o:p></pre>
<pre>Cc: Roger Noble <a href="mailto:roger@zegami.com"><roger@zegami.com></a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I’ve been look at a few examples from the link Josh sent to me and<o:p></o:p></pre>
<pre>there are quite a lot! What would be a good data set to get import<o:p></o:p></pre>
<pre>into Zegami from IDR? I am thinking a set that has decent metadata<o:p></o:p></pre>
<pre>and a study that people are more familiar with that would make an<o:p></o:p></pre>
<pre>interesting use case.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Kind regards,<o:p></o:p></pre>
<pre>Steve<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>From: Stephen Taylor<o:p></o:p></pre>
<pre>Sent: 10 June 2016 14:25<o:p></o:p></pre>
<pre>Cc: Roger Noble <a href="mailto:roger@zegami.com"><roger@zegami.com></a>; '<a href="mailto:e.x.williams@dundee.ac.uk">e.x.williams@dundee.ac.uk</a>'<o:p></o:p></pre>
<pre><a href="mailto:e.x.williams@dundee.ac.uk"><e.x.williams@dundee.ac.uk></a><o:p></o:p></pre>
<pre>Subject: RE: [IDR Project] Zegami / IDR<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi all,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I am interested generally in getting data in and out of OMERO from<o:p></o:p></pre>
<pre>both internal and external. Over a WAN the images are less of an issue<o:p></o:p></pre>
<pre>since they are streamed on demand but large metadata on the other hand<o:p></o:p></pre>
<pre>can get out of hand since it all has to be loaded completely into<o:p></o:p></pre>
<pre>Zegami’s database.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Currently I do “OMERO project” to “Zegami collection” using a Zegami<o:p></o:p></pre>
<pre>export script (modified version of the OMERO batch export script).<o:p></o:p></pre>
<pre>This takes a project or selection of images from OMERO and produces<o:p></o:p></pre>
<pre>thumbnails and data in tab delimited Zegami format and then I manually<o:p></o:p></pre>
<pre>import that into Zegami for processing. The OMERO id is preserved so I<o:p></o:p></pre>
<pre>can link to the original image in OMERO using the OMERO web client. I<o:p></o:p></pre>
<pre>only export certain metadata currently (filenames and OMERO tags) and<o:p></o:p></pre>
<pre>my plan is to make this more comprehensive and allow MapAnnotations<o:p></o:p></pre>
<pre>and Tables to be exported using this mechanism as well. I need to find<o:p></o:p></pre>
<pre>out more how to query these data types. Since we have internal<o:p></o:p></pre>
<pre>projects at Oxford that need this I’d like to finish this and make<o:p></o:p></pre>
<pre>that plugin freely available for other OMERO users to publish their<o:p></o:p></pre>
<pre>data in Zegami.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Longer term for IDR/Zegami<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>One of your team (apologies I didn’t get his name but he was doing<o:p></o:p></pre>
<pre>OMERO/ImageJ in the Unconference session) suggested we just stream in<o:p></o:p></pre>
<pre>the thumbnail and just have 1 level (i.e. no zoom) and when you want<o:p></o:p></pre>
<pre>to see the image just open it up in OMERO. This would not be as nice<o:p></o:p></pre>
<pre>to use but may be sufficient for HCS and would allow you to use<o:p></o:p></pre>
<pre>Zegami’s facet based query engine and would be probably little (no?)<o:p></o:p></pre>
<pre>work for you guys. We need to test this to see what it looks like and<o:p></o:p></pre>
<pre>it assumes OMERO can supply a unique thumbnail URL for each image and<o:p></o:p></pre>
<pre>that the metadata will provide a primary key so that we can get to<o:p></o:p></pre>
<pre>this image via a thumbnail id. To get at the metadata Josh and Eleanor<o:p></o:p></pre>
<pre>said they were thinking of making the CSV downloadable for a<o:p></o:p></pre>
<pre>collection, which could be loaded into Zegami on the fly (we have<o:p></o:p></pre>
<pre>instances where we dynamically load metadata via URL already).<o:p></o:p></pre>
<pre>However, major caveat is on how well this would perform over a WAN<o:p></o:p></pre>
<pre>with a large amount of data.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>BTW we have developer docs for Zegami for those interested at:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a href="https://support.zegami.com/hc/en-us/categories/200350657-Developers">https://support.zegami.com/hc/en-us/categories/200350657-Developers</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>and would welcome feedback.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Kind regards and thanks,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Steve<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>From: Jason Swedlow (Staff) [<a href="mailto:j.r.swedlow@dundee.ac.uk">mailto:j.r.swedlow@dundee.ac.uk</a>]<o:p></o:p></pre>
<pre>Sent: 08 June 2016 13:09<o:p></o:p></pre>
<pre>Cc: Eleanor Williams (Staff) <a href="mailto:e.x.williams@dundee.ac.uk"><e.x.williams@dundee.ac.uk></a><o:p></o:p></pre>
<pre>Subject: Re: [IDR Project] Zegami / IDR<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Josh et al—<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>My two cents— can we consider this use case from an external users’<o:p></o:p></pre>
<pre>perspective, mindful that distribution of such a solution would<o:p></o:p></pre>
<pre>definitely cause us to consider how we ship thumbnails, handle<o:p></o:p></pre>
<pre>straws, etc.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers,<o:p></o:p></pre>
<pre>Jason<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>On Wed, Jun 8, 2016 at 1:31 PM, Josh Moore <a href="mailto:josh@glencoesoftware.com"><josh@glencoesoftware.com></a> wrote:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Stephen,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>On Wed, Jun 8, 2016 at 9:52 AM, Stephen Taylor<o:p></o:p></pre>
<pre><a href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a> wrote:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Hi Josh,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Yes! What would be the best way of bulk downloading the thumbnails for a screen or plate<o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre>Interesting question. Guess the reverse question is: do you want to do<o:p></o:p></pre>
<pre>this as an external user or as if you had access to the OMERO?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>( I notice the "Run Script" button isn't active ).<o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre>Correct. This server is stripped down in several ways as a public resource.<o:p></o:p></pre>
<pre>~J.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Kind regards,<o:p></o:p></pre>
<pre>Steve<o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: Josh Moore [<a href="mailto:josh@glencoesoftware.com">mailto:josh@glencoesoftware.com</a>]<o:p></o:p></pre>
<pre>Sent: 08 June 2016 08:07<o:p></o:p></pre>
<pre>To: Stephen Taylor <a href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a><o:p></o:p></pre>
<pre>Cc: Eleanor Williams <a href="mailto:exwilliams@dundee.ac.uk"><exwilliams@dundee.ac.uk></a>;<o:p></o:p></pre>
<pre><a href="mailto:e.x.williams@dundee.ac.uk">e.x.williams@dundee.ac.uk</a>; <a href="mailto:j.a.moore@dundee.ac.uk">j.a.moore@dundee.ac.uk</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Subject: Re: Zegami / IDR<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Stephen,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>On Wed, Jun 8, 2016 at 8:40 AM, Stephen Taylor<o:p></o:p></pre>
<pre><a href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a> wrote:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Hi Eleanor,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Thanks very useful. Is the web site publically available?<o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre>You mean <a href="http://idr-demo.openmicroscopy.org/webclient">http://idr-demo.openmicroscopy.org/webclient</a> ?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers,<o:p></o:p></pre>
<pre>~Josh<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Kind regards and thanks,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Steve<o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>From: Eleanor Williams [<a href="mailto:exwilliams@dundee.ac.uk">mailto:exwilliams@dundee.ac.uk</a>]<o:p></o:p></pre>
<pre>Sent: 07 June 2016 11:09<o:p></o:p></pre>
<pre>To: Stephen Taylor <a href="mailto:stephen.taylor@imm.ox.ac.uk"><stephen.taylor@imm.ox.ac.uk></a>;<o:p></o:p></pre>
<pre><a href="mailto:e.x.williams@dundee.ac.uk">e.x.williams@dundee.ac.uk</a>; <a href="mailto:j.a.moore@dundee.ac.uk">j.a.moore@dundee.ac.uk</a><o:p></o:p></pre>
<pre>Subject: Re: Zegami / IDR<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Stephen<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Here is a link to our workshop presentation but it describes how to<o:p></o:p></pre>
<pre>get the data into omero rather than out.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a 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><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>We will be adding the annotation.csv files as attachments to each<o:p></o:p></pre>
<pre>screen over the next couple of weeks.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Let us know if you have any more questions.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Best regards<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Eleanor<o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>On 07/06/2016 10:41, Stephen Taylor wrote:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Eleanor and Josh,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Great to meet you both at the OME meeting last week.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I'd be interested in trying get some data into Zegami from IDR. I<o:p></o:p></pre>
<pre>missed your Unmeeting (ironically I was demoing Zegami) where I think<o:p></o:p></pre>
<pre>you went into some of the technical details. Can you send me the link<o:p></o:p></pre>
<pre>to your presentation please?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Kind regards and thanks,<o:p></o:p></pre>
<pre>Steve<o:p></o:p></pre>
</blockquote>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>ome-devel mailing list<o:p></o:p></pre>
<pre><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><o:p></o:p></pre>
<pre><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Eleanor Williams PhD<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Data Annotator/Software Engineer<o:p></o:p></pre>
<pre>Centre for Gene Regulation and Expression<o:p></o:p></pre>
<pre>University of Dundee, UK<o:p></o:p></pre>
<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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