<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><div><div>Hi Christophe,</div><div><br></div><div><div><blockquote type="cite" class="clean_bq" style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">Congratulations also from our side :)</div></div></blockquote></div><p>Thanks a lot.</p><p><br></p></div></div><div><div><blockquote type="cite" class="clean_bq" style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">- How did you save the layers? Did you use different images, or channels or something more internal to OMERO?</div></div></blockquote></div><p>The extra layers with the data analysis results were added as channels. We have used a pattern file (https://www.openmicroscopy.org/site/support/bio-formats5.1/formats/pattern-file.html) to group the '.tifs' together and import them to OMERO as a single image.</p><div><div><blockquote type="cite" class="clean_bq" style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">- How do you make the dataset public? I assume people are working with images in private setting for quite some time and then at the date of publication, the images are made publically available.</div></div></blockquote></div><p>At present this OMERO instance is only dedicated to data publication. I have followed the OME documentation on how to make the data public: http://www.openmicroscopy.org/site/support/omero5.1/developers/Web/PublicData.html. In our setup the public user does not own any of the data. The data is owned by other users that are also members of the "public-group". This is to make sure that I could make the data private prior the publication date. On the publication date I simply moved the data from a private group - private in a sense that the public users is not a member of it - to the "public-group", making the image publicly available - accessible by the public user.</p><div><div><blockquote type="cite" class="clean_bq" style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">- Is the code of the webclient available on some public repo?</div></div></blockquote></div><p>Currently the code is not available anywhere beside the website itself :).</p><div><div><blockquote type="cite" class="clean_bq" style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">- Did you carry out any modifications on the server side?</div></div></blockquote></div><p>We are running out-of-the-box OMERO 5.1 with no modifications. The only modifications happened to the Viewer. To be more precise I have stripped the Toolbox from the OMERO Viewer and added custom buttons to group the channels together. Some of the data analysis results are spread over 3 channels and they need to be toggled ON and OFF together.</p><div><div><blockquote type="cite" class="clean_bq" style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">- Will you guarantee availability of data over couple of years? 10? more?</div></div></blockquote></div><p>We are obliged by the funding body of this project (BBSRC) to keep this data for 10 years, so it will be around for at least 10 years.</p><p><br></p><p>Cheers,</p><p>Emil</p><div><br class="Apple-interchange-newline"></div></div></div></div></div></div></div> <br><p style="color:#000;">On 7 April 2015 at 14:35:15, Christophe TREFOIS (<a href="mailto:christophe.trefois@uni.lu">christophe.trefois@uni.lu</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div></div><div>
<title></title>
Hi Emil,
<div class=""><br class=""></div>
<div class="">Congratulations also from our side :)</div>
<div class=""><br class=""></div>
<div class="">Based on our chat, I will formalise a couple of
questions that might benefit the whole community, especially about
the process that you took to get this nice tool ready.</div>
<div class=""><br class=""></div>
<div class="">- How did you save the layers? Did you use different
images, or channels or something more internal to OMERO?</div>
<div class="">- How do you make the dataset public? I assume people
are working with images in private setting for quite some time and
then at the date of publication, the images are made publically
available.</div>
<div class="">- Is the code of the webclient available on some
public repo?</div>
<div class="">- Did you carry out any modifications on the server
side?</div>
<div class="">- Will you guarantee availability of data over couple
of years? 10? more?</div>
<div class=""><br class=""></div>
<div class="">Kind regards,</div>
<div class=""><br class=""></div>
<div class="">—</div>
<div class="">Christophe</div>
<div class="">
<div class="">
<p style="font-family: Arial, sans-serif; font-size: 10pt; line-height: 16px; color: rgb(33, 33, 33);" class=""><span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">Dr Christophe Trefois, Dipl.-Ing.</span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span></p>
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<blockquote type="cite" class="">
<div class="">On 03 Apr 2015, at 15:46, Jason Swedlow (Staff)
<<a href="mailto:j.r.swedlow@dundee.ac.uk" class="">j.r.swedlow@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Calibri, sans-serif; font-size: 14px;" class="">
<div class="">Hi Emil</div>
<div class=""><br class=""></div>
<div class="">Thanks for this update, and congrats on the
publication of your paper and this data set. It’s a great
example of the kind of thing we want to enable with OMERO and
Bio-Formats.</div>
<div class=""><br class=""></div>
<div class="">Several people have asked us to document the set-up
and configuration of OMERO as a public data sharing repository.
We’ll definitely try to capture your experience, as well as
several others in this doc and get this included in the 5.1.1
release.</div>
<div class=""><br class=""></div>
<div class="">Congrats again on this great work.</div>
<div class=""><br class=""></div>
<div class="">Cheers,</div>
<div class=""><br class=""></div>
<div class="">Jason</div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class="">On 31/03/2015 15:39, "Emil Rozbicki (Staff)"
<<a href="mailto:e.j.rozbicki@dundee.ac.uk" class="">e.j.rozbicki@dundee.ac.uk</a>> wrote:</div>
<div class=""><br class=""></div>
<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;" class="" type="cite">
<div class="">Dear OME developers,</div>
<div class=""><br class=""></div>
<div class="">I would like to share with you our latest achivement
which couldn't have happened without your effort. We have
succesfully published a light-sheet microscopy dataset together
with the analysis results using OMERO as a publication platform.
The dataset is avaiable here: <a href="http://omero-cjw.lifesci.dundee.ac.uk/10.15132.10000100/" class="">http://omero-cjw.lifesci.dundee.ac.uk/10.15132.10000100/</a> and
is published alongside Nature Cell Biology manuscipt <a href="http://dx.doi.org/10.1038/ncb3138" class="">http://dx.doi.org/10.1038/ncb3138</a>.</div>
<div class=""><br class=""></div>
<div class="">Some technical details:</div>
<div class="">The original dataset has almost 100 Gigapixels while
the OMERO available image holds half of it. The OMERO image
contains one channel with the microscopy data and further 18
channels with the analysis results. The image served by OMERO is
around 50GB, including all analysis results. The dataset is
downloadable from the website with substantially compressed
analysis outcomes taking it all down to 10GB.</div>
<div class=""><br class=""></div>
<div class="">I would like to thank you All for making the data
publication so easy.</div>
<div class=""><br class=""></div>
<div class="">Regards,</div>
<div class="">Emil Rozbicki</div>
<div class=""><br class=""></div>
<div class="">The University of Dundee is a registered Scottish
Charity, No: SC015096</div>
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<div class=""><br class=""></div>
</blockquote>
<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is
a registered Scottish Charity, No: SC015096</span></div>
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