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Hi Jake,
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<div class=""> Just to clarify a little:</div>
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<div class=""> The “12k x 12k” pixel download limit is only for “Export as TIFF/JPEG/PNG” and can be configured </div>
<div class=""><a href="https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/config.html#omero-client-download-as-max-size" class="">https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/config.html#omero-client-download-as-max-size</a></div>
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</div>
<div class="">This limit is dependent on the maximum plane size that can be rendered by the rendering engine,</div>
<div class="">since we get an OOM error in omeis.providers.re.RGBIntBuffer.</div>
<div class="">You can try to see if your infrastructure might support a higher limit.</div>
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</div>
<div class="">Export as OME-TIFF doesn’t support tiled images (default limit for this is about 3k x 3k but is also configurable).</div>
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</div>
<div class="">However, there is no fixed limit for downloads of the original image data.</div>
<div class="">This is purely dependent on your bandwidth and other infrastructure.</div>
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</div>
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</div>
<div class="">The changes to the “Images from ROIs” script that adds support for big images are in this PR:</div>
<div class=""><a href="https://github.com/ome/scripts/pull/115" class="">https://github.com/ome/scripts/pull/115</a></div>
<div class="">If you are happy to download the latest version of that script and update it on your server</div>
<div class="">then you wouldn’t have to wait for back-porting and point release.</div>
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<div class="">Regards,</div>
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<div class=""> Will.</div>
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<blockquote type="cite" class="">
<div class="">On 25 Oct 2016, at 20:09, Jake Carroll <<a href="mailto:jake.carroll@uq.edu.au" class="">jake.carroll@uq.edu.au</a>> wrote:</div>
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<span style="font-size: 11pt;" class="">Hi Jean-Marie.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<span style="font-size: 11pt;" class="">Thanks for getting back to me. Most appreciated.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<i class=""><span style="font-size: 11pt;" class="">>> We currently have a limit on the size of the image that can downloaded.<o:p class=""></o:p></span></i></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<span style="font-size: 11pt;" class="">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 class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<i class=""><span style="font-size: 11pt;" class="">>> 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 class=""></o:p></span></i></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<span style="font-size: 11pt;" class="">Absolutely correct, yes.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<i class=""><span style="font-size: 11pt;" class="">>> A new script is available in OMERO 5.3, <a href="https://github.com/ome/scripts/pull/115" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/ome/scripts/pull/115</a> to
generate tiles images from ROIs<o:p class=""></o:p></span></i></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<span style="font-size: 11pt;" class="">That could be exceedingly useful to us and I’d welcome it.<o:p class=""></o:p></span></div>
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<i class=""><span style="font-size: 11pt;" class=""> </span></i></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<i class=""><span style="font-size: 11pt;" class="">>> We are considering a 5.2.7 release to add support for ice 3.6.3<o:p class=""></o:p></span></i></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<i class=""><span style="font-size: 11pt;" class="">>> So we could certainly back port the script mentioned above if it solved some of the issues.<o:p class=""></o:p></span></i></div>
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<i class=""><span style="font-size: 11pt;" class=""> </span></i></div>
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<span style="font-size: 11pt;" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<span style="font-size: 11pt;" class="">Regards, and thanks again for your response. It is heartening.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">-jc<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<b class=""><span style="" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="" class="">"Jean-Marie Burel (Staff)" <<a href="mailto:j.burel@dundee.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">j.burel@dundee.ac.uk</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Wednesday, 26 October 2016 at 07:02<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>Jake Carroll <<a href="mailto:jake.carroll@uq.edu.au" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">jake.carroll@uq.edu.au</a>>, "<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>"
<<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:<span class="Apple-converted-space"> </span></b>"Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">s.besson@dundee.ac.uk</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: 12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?</span><span style="" class=""><o:p class=""></o:p></span></div>
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Dear Jake<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
We currently have a limit on the size of the image that can downloaded.<o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
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 class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
A new script is available in OMERO 5.3, <a href="https://github.com/ome/scripts/pull/115" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/ome/scripts/pull/115</a> to generate tiles images from ROIs<o:p class=""></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
We are considering a 5.2.7 release to add support for ice 3.6.3<o:p class=""></o:p></div>
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<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
So we could certainly back port the script mentioned above if it solved some of the issues.<o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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Cheers<o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
Jmarie<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class=""><span style="font-size: 11pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 11pt;" class="">Jake Carroll <<a href="mailto:jake.carroll@uq.edu.au" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">jake.carroll@uq.edu.au</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Tuesday, 25 October 2016 03:50<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:<span class="Apple-converted-space"> </span></b>jmarie burel <<a href="mailto:j.burel@dundee.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">j.burel@dundee.ac.uk</a>>, "Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">s.besson@dundee.ac.uk</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?<o:p class=""></o:p></span></div>
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<span lang="EN-AU" style="font-size: 11pt;" class="">Hi all.</span><o:p class=""></o:p></div>
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<span lang="EN-AU" style="font-size: 11pt;" class=""> </span><o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">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 class=""></o:p></div>
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<span style="font-size: 11pt;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt;" class="">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 class=""></o:p></div>
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<span style="font-size: 11pt;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt;" class="">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 class=""></o:p></div>
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<span lang="EN-AU" style="font-size: 11pt;" class=""> </span><o:p class=""></o:p></div>
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<span lang="EN-AU" style="font-size: 11pt;" class="">Thank you.</span><o:p class=""></o:p></div>
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<span lang="EN-AU" style="font-size: 11pt;" class=""> </span><o:p class=""></o:p></div>
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<span lang="EN-AU" style="font-size: 11pt;" class="">-jc</span><o:p class=""></o:p></div>
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