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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">Dear Will,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">It worked partially.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">We will create a bug submission on the github page shortly.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The quick breakdown is that the page size can be smaller than the imported image resulting in a silent error.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Eg, the javascript complains about some negative x-y values.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">To make it work, we simply have to increase the page size to something bigger and then it works perfectly.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">My colleague Yohan Jarosz created a pull request for this by adding more paper formats in the dropdowns of the Django
templates.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> William Moore [mailto:will@lifesci.dundee.ac.uk]
<br>
<b>Sent:</b> jeudi 30 octobre 2014 00:40<br>
<b>To:</b> Christophe TREFOIS<br>
<b>Cc:</b> ome-devel@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> Re: [ome-devel] OMERO.figure limitations<o:p></o:p></span></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">Hi Christophe,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Since OMERO.figure does not feature a tiled image viewer, it only works with<o:p></o:p></p>
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<p class="MsoNormal">single planes of the whole image at a time.<o:p></o:p></p>
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<p class="MsoNormal">Therefore, this limits the size of images that can be loaded.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">However, there is no strict limit on the maximum size that can be used.<o:p></o:p></p>
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<p class="MsoNormal">We can load entire planes larger than the "Big Image" threshold where images<o:p></o:p></p>
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<p class="MsoNormal">become tiled in OMERO.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Currently, I've chosen an arbitrary limit of 5000 x 5000 pixels (or equivalent) since 4k x 4k images<o:p></o:p></p>
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<p class="MsoNormal">seemed to work OK.<o:p></o:p></p>
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<p class="MsoNormal">This is hard-coded, E.g. in the 1.0.0 release it's at:<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 href="https://github.com/will-moore/figure/blob/develop/static/figure/js/figure-1.0.0.js#L2621">https://github.com/will-moore/figure/blob/develop/static/figure/js/figure-1.0.0.js#L2621</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">if (data.size.width * data.size.height > 5000 * 5000) {<o:p></o:p></p>
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<p class="MsoNormal"> alert("Image '" + data.meta.imageName + "' is too big for OMERO.figure");<o:p></o:p></p>
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<p class="MsoNormal"> return;<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">You could try to increase this limit in figure/static/figure/js/figure-1.0.0.js<o:p></o:p></p>
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<p class="MsoNormal">to see if 5000 x 10000 image planes can be loaded.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Perhaps you can try this first…<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Log in to the web client and find an example image of 10000 x 5000 pixels.<o:p></o:p></p>
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<p class="MsoNormal">Then edit <your-server> and <image-id> in this url<o:p></o:p></p>
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<p class="MsoNormal">to load an entire plane.<o:p></o:p></p>
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<p class="MsoNormal"> <your-server>/webgateway/render_image/<image-id>/0/0/<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This will give you some idea of the performance of this.<o:p></o:p></p>
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<p class="MsoNormal">If performance is not too bad, then feel free to increase the limit above,<o:p></o:p></p>
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<p class="MsoNormal">although bear in mind that performance will be worse at locations with lower bandwidth.<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">To fully support large tiled images in OMERO.figure, we'd need a proper tile-based<o:p></o:p></p>
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<p class="MsoNormal">image viewer. But this would be quite a lot of work.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">One alternative is for your users to draw rectangle ROIs on their big images in Insight <o:p></o:p></p>
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<p class="MsoNormal">(ROIs of 3000 x 3000 or less) then use the script: <o:p></o:p></p>
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<p class="MsoNormal">util script > Images From ROIs <o:p></o:p></p>
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<p class="MsoNormal">to create new images based on those regions. These can then be imported into OMERO.figure.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Hope that helps,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Will.<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"><o:p> </o:p></p>
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<p class="MsoNormal">On 29 Oct 2014, at 17:32, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu">christophe.trefois@uni.lu</a>> wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dear all,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Does anybody know the limitation in terms of pixel size of OMERO.figure ?</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Our researchers love this new tool but sometimes use stitched images which can be around 10.000 x 5.000 pixels which doesn’t seem to work with OMERO.figure.</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Can this setting be changed anywhere?</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Best,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#404040">................................................................................</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#404040">Dr. Christophe TREFOIS,<span class="apple-converted-space"> </span>Dipl.-Ing.</span></b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#404040"><br>
</span><i><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#404040">Doctor in Biology</span></i><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:3.0pt"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#404040">Senior Technical Specialist</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#404040">UNIVERSITÉ DU LUXEMBOURG</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#404040">LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#404040">Campus Belval | House of Biomedicine</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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