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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for submitting your data.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Having tested it in a variety of different OS/Fiji and Bio-Formats combinations,<o:p></o:p></p>
<p class="MsoNormal">we were finally able to reproduce the issue on Windows 10.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This performance issue seems to be windows specific and I have created a card to follow up on that.<o:p></o:p></p>
<p class="MsoNormal"><a href="https://trello.com/c/rgUGN9Ll/187-zvi-windows-performance-issuefiji">https://trello.com/c/rgUGN9Ll/187-zvi-windows-performance-issuefiji</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This will get looked into at the earliest.<o:p></o:p></p>
<p class="MsoNormal">Thank you again for submitting your data and the plots as requested.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Balaji <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of "Favre, Alban" <Alban.Favre@ggbearings.com><br>
<b>Reply-To: </b>OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Date: </b>Monday, 11 September 2017 at 07:39<br>
<b>To: </b>OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject: </b>Re: [ome-users] ZVI opening help</span><span style="font-size:12.0pt;color:black;mso-fareast-language:EN-GB"><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"><span lang="EN-US" style="color:#1F497D">Hi, </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">The file “</span><span lang="EN-US">mozaicDP4.zvi »<span style="color:#1F497D"> is uploaded,</span></span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thank you again for your support .</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Regards</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Alban</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;mso-fareast-language:FR">De :</span></b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;mso-fareast-language:FR"> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>De la part de</b> Balaji Ramalingam (Staff)<br>
<b>Envoyé :</b> vendredi 8 septembre 2017 15:46<br>
<b>À :</b> OME User Support List<br>
<b>Objet :</b> Re: [ome-users] ZVI opening help</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Hi Alban,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thank you for sharing the results of the macro.<o:p></o:p></p>
<p class="MsoNormal">It clearly looks like the first iteration takes longer than expected.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Unfortunately, we are unable to reproduce the same locally, with the ‘zvi’ files that we have.<o:p></o:p></p>
<p class="MsoNormal">Could you please upload the problematic file to the following link?<o:p></o:p></p>
<p class="MsoNormal"><a href="https://www.openmicroscopy.org/qa2/qa/upload/">https://www.openmicroscopy.org/qa2/qa/upload/</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">This would help us troubleshoot the issue in better detail.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Balaji<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf
of "Favre, Alban" <<a href="mailto:Alban.Favre@ggbearings.com">Alban.Favre@ggbearings.com</a>><br>
<b>Reply-To: </b>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<b>Date: </b>Thursday, 7 September 2017 at 14:38<br>
<b>To: </b>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<b>Subject: </b>Re: [ome-users] ZVI opening help</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D">Hi Balaji,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Sorry for the delay, it’s holiday period in France.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I enclosed the resultant pot, and as you can see the first iteration is quite long.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I used the 5.6 version form 14 august with Fiji 1.51p.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">For the moment I simply used the same function as you in my macro code :</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">run("Bio-Formats Importer", "open=/Users/a_favre/Desktop/mozaicDP4.zvi autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thanks in advance </span>
<o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Alban</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;mso-fareast-language:FR">De :</span></b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;mso-fareast-language:FR"> ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]
<b>De la part de</b> Balaji Ramalingam (Staff)<br>
<b>Envoyé :</b> vendredi 25 août 2017 18:30<br>
<b>À :</b> OME User Support List<br>
<b>Objet :</b> Re: [ome-users] ZVI opening help</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thank you for sharing your issue.<o:p></o:p></p>
<p class="MsoNormal">We were unable to reproduce the issue locally with Bio-Formats 5.6.0, Fiji.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I have attached the macro snippet that we used to resolve the time taken over 20 iterations and the resultant plot in this thread,<o:p></o:p></p>
<p class="MsoNormal">and we did not see a significant difference in the time taken over the multiple iterations as well.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">It would be great if you could please do the following,<o:p></o:p></p>
<p class="MsoNormal">1) run the above macro in your Fiji installation (on one of your files which has had issues) and send us a screenshot of the resultant plot<o:p></o:p></p>
<p class="MsoNormal">2) Share your macro code as well.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">This would help us troubleshoot the issue in better detail.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Balaji<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf
of "Favre, Alban" <<a href="mailto:Alban.Favre@ggbearings.com">Alban.Favre@ggbearings.com</a>><br>
<b>Reply-To: </b>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<b>Date: </b>Thursday, 24 August 2017 at 07:33<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>Subject: </b>[ome-users] ZVI opening help</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p style="margin-top:0in;background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Hi,<br>
I am using the bioformat plugin to open ZVI images in a macro.<br>
When I launch it, it takes around 30s just to analyse the image and 2s to really open it.... and half of the time it even do no open anything.<br>
Moreover when its working it open a stack with three different color chanels (c) whereas all the slices are similar.<br>
is there a way to speed up and make more robust the ZVI opening by preventing stacking or something else?</span><o:p></o:p></p>
<p style="margin-top:0in;background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Thanks in advance!</span><o:p></o:p></p>
<p style="margin-top:0in;background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">I am using :</span><o:p></o:p></p>
<p style="margin-top:0in;background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Bioformat 5.6.0</span><o:p></o:p></p>
<p style="margin-top:0in;background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Fiji/imagej 1.51P</span><o:p></o:p></p>
<p style="margin-top:0in;background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">below an example of my metadata</span><o:p></o:p></p>
<p style="background:white;font-variant-ligatures: normal;font-variant-caps: normal;orphans: 2;text-align:start;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<em><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">BitsPerPixel = 16</span></em><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222"><br>
_ DimensionOrder = XYCZT_<br>
_ IsInterleaved = true_<br>
_ IsRGB = false_<br>
_ LittleEndian = true_<br>
_ PixelType = uint16_<br>
_ Series 0 Name = RB152.1.2.11F_RB152.1.2.11D.zvi_<br>
_ SizeC = 3_<br>
_ SizeT = 1_<br>
_ SizeX = 11034_<br>
_ SizeY = 15913_<br>
_ SizeZ = 1_<br>
<em><span style="font-family:"Helvetica",sans-serif">AxioCam Black Reference = false</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">AxioCam Color Model = true</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">AxioCam Resolution = 8217</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">BlackValue = 0.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera = AxioCamICc5</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Acquisition Time 0 </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 2017-08-23T10:26:50.842</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Adapter Magnification = 0.63</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Bit Depth = 36</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Frame Height = 2056</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Frame Width = 2452</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Framestart Left = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Framestart Top = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Camera Shading Correction = true</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">CameraExposureTimeCalculationControl = 1.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">CameraFrameImageOrientation = 4</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">CameraFramePixelDistance = 3.45</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">CameraFrameScalingFactor = 1.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">CameraLiveScalingFactor = 1.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ContrastManagerMode = 3</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Dazzle Protection Active = true</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">DeviceScalingName = AxioCamICc5</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Document Type = Image</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Exposure Time [ms] = 12.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">File Date = 1969-12-31T23:59:59.999</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Filename = RB152.1.2.11F</span></em>RB152.1.2.11D.zvi_<br>
<em><span style="font-family:"Helvetica",sans-serif">Focus Position = 273.45</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Focus Position 0 = 273.45</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Focus calibrated = false</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">FocusDepth = 8.8</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">GammaValue = 0.45</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">GammaValue 0 = 0.45</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Image Channel Index </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Image Index S = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Image Index T = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Image Index Z 0 = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Image Memory Usage (RAM) = 1053504316</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Image acquisition Index = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageHeight = 15913</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageRelativeTime 0 </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 0.0 d</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageRelativeTime1 0 </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 0.0 d</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageRelativeTime2 0 </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 0.0 d</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageRelativeTime3 0 </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 0.0 d</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageRelativeTime4 0 </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 0.0 d</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageTile Index = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ImageWidth = 11034</span></em><br>
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<em><span style="font-family:"Helvetica",sans-serif">(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51p; Java 1.8.0</span></em>66 [64-bit]; Windows 10 10.0; 3250MB of 60000MB (5%)_<br>
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<em><span style="font-family:"Helvetica",sans-serif">Title: RB152.1.2.11F</span></em>RB152.1.2.11D.zvi_<br>
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<em><span style="font-family:"Helvetica",sans-serif">Image: 1/3 (c:1/3 - RB152.1.2.11F</span></em>RB152.1.2.11D)_<br>
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<em><span style="font-family:"Helvetica",sans-serif">Path: D:\Results</span></em>micro\PD276\RB152.1.2.11F_RB152.1.2.11D.zvi_<br>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">Alban Favre</span></b><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">R&D Engineer - Product & Process Development</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:FR"><img border="0" width="188" height="82" id="_x0000_i1025" src="cid:image001.gif@01D32D1D.7FAC82F0"></span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">GGB France EURL - Annecy</span></b><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">65 Chemin de la Prairie</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">BP2074</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">74009 Annecy</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">France</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:gray;mso-fareast-language:FR">Tel:
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR">+33450336623</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR"><a href="mailto:Alban.Favre@ggbearings.com">Alban.Favre@ggbearings.com</a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:FR"><a href="http://www.ggbearings.com">http://www.ggbearings.com</a></span><o:p></o:p></p>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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