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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Jean-Marie.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks for getting back to me. Most appreciated.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt">>> We currently have a limit on the size of the image that can downloaded.<o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Yes, and this worries people locally a great deal. They feel like their data “becomes trapped”. They can absolutely get the data IN to OMERO, but from a preservation perspective it becomes questionable to
them if they can’t get *<b>the same</b>* data back out. From a data-governance and provenance perspective, I’d really like to see this fixed. It would allow us to adhere to several strict federal regulations and laws by doing so – and it’d make the scientists
feel a lot more secure in their knowledge that OMERO is an authoritative data sink. If data can only go “one way” it represents a risk to scientists in some respects, from a digital preservation and data governance perspective, as you can appreciate.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt">>> By ROI extraction, are you thinking of creating ROI on some of those large images and “cropping” to generate a new image then download that image?<o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Absolutely correct, yes.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt">>> A new script is available in OMERO 5.3, <a href="https://github.com/ome/scripts/pull/115">https://github.com/ome/scripts/pull/115</a> to generate tiles images from ROIs<o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">That could be exceedingly useful to us and I’d welcome it.<o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt"><o:p> </o:p></span></i></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt">>> We are considering a 5.2.7 release to add support for ice 3.6.3<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt">>> So we could certainly back port the script mentioned above if it solved some of the issues.<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt"><o:p> </o:p></span></i></p>
<p class="MsoNormal"><span style="font-size:11.0pt">You’d absolutely make a lot of progress for us by doing this and we’d be exceedingly appreciative. These things have been long-term niggling issues with complete OMERO adoption and total trust for a very long
time. Fixing these things would boost confidence in the researchers and make OMERO a more ubiquitous platform for all.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Regards, and thanks again for your response. It is heartening.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-jc<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">"Jean-Marie Burel (Staff)" <j.burel@dundee.ac.uk><br>
<b>Date: </b>Wednesday, 26 October 2016 at 07:02<br>
<b>To: </b>Jake Carroll <jake.carroll@uq.edu.au>, "ome-users@lists.openmicroscopy.org.uk" <ome-users@lists.openmicroscopy.org.uk><br>
<b>Cc: </b>"Sebastien Besson (Staff)" <s.besson@dundee.ac.uk><br>
<b>Subject: </b>Re: 12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman""><o:p> </o:p></span></p>
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<p class="MsoNormal">Dear Jake<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We currently have a limit on the size of the image that can downloaded.<o:p></o:p></p>
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<p class="MsoNormal">By ROI extraction, are you thinking of creating ROI on some of those large images and “cropping” to generate a new image then download that image?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">A new script is available in OMERO 5.3, <a href="https://github.com/ome/scripts/pull/115">https://github.com/ome/scripts/pull/115</a> to generate tiles images from ROIs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We are considering a 5.2.7 release to add support for ice 3.6.3<o:p></o:p></p>
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<p class="MsoNormal">So we could certainly back port the script mentioned above if it solved some of the issues.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Jmarie<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;color:black">From: </span></b><span style="font-size:11.0pt;color:black">Jake Carroll <<a href="mailto:jake.carroll@uq.edu.au">jake.carroll@uq.edu.au</a>><br>
<b>Date: </b>Tuesday, 25 October 2016 03:50<br>
<b>To: </b>"<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<b>Cc: </b>jmarie burel <<a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>>, "Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk">s.besson@dundee.ac.uk</a>><br>
<b>Subject: </b>12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt">Hi all.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I was just wondering if there had been any consideration given to the 12k x 12k pixel limit on certain ROI Extraction/manipulation semantics in OMERO 5.3 for your road map? From what I can tell, in OMERO 5.2.x
series code, there still exists limitations on how large an extraction of an ROI can be, and the ability to manipulate data beyond 12k x 12k pixel wide dimensions.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">We’re now on a daily basis, getting significant requests/complaints from people ingesting very big things (100k x 100k pixel style stuff) who’d dearly love to work with their data – but can’t ROI extract,
nor work with it anymore, due to the fact that there seems to be a 12k x 12k limit on file format transforms (I assume it is a BIOFormats thing/BIgTIFF thing/OMETIFF limitation).</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Would like to know if any progress had been made with this limitation – it’d kind of liberate OMERO for us in an amazing way/really make a lot of scientists smile…</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt">Thank you.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt">-jc</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman";mso-fareast-language:EN-GB"><br>
</span><span style="font-size:10.0pt;font-family:"Times New Roman";mso-fareast-language:EN-GB">The University of Dundee is a registered Scottish Charity, No: SC015096</span><span style="font-family:"Times New Roman";mso-fareast-language:EN-GB">
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