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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 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 <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>Thursday, 24 August 2017 at 07:33<br>
<b>To: </b>"ome-users@lists.openmicroscopy.org.uk" <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject: </b>[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>
</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>
<em><span style="font-family:"Helvetica",sans-serif">Last modified by = GGBNCYATR</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">LightManagerEnabled = true</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Lightmanager Mode = 2</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Location = D:\Results</span></em>micro\PD276\RB152.1.2.11F_RB152.1.2.11D.zvi_<br>
<em><span style="font-family:"Helvetica",sans-serif">Microscope Name = Axio Imager.M2</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Microscope Port = 5</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">MicroscopeIllumination = -1</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">MicroscopeMagnification = 6.3</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">MicroscopeType = 56</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Number Raw Count = 1</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">NumberOfRawImages = 1</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ObjectType = 1</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective Contrast Method = 2</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective ID = Objective.422342-9960-000</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective Immersion Type = 1</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective Magnification = 10.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective N.A. = 0.25</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective Name = EC Epiplan-Neofluar 10x/0.25 HD DIC M27</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective Turret Position = 3</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Objective Working Distance = 9000.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Ocular Total Magnification = 100.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Original Stage Position X = 23936.187905089406</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Original Stage Position X 0 = 23936.187905089406</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Original Stage Position Y = -37035.10359353507</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Original Stage Position Y 0 = -37035.10359353507</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Parfocal Correction = true</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">PixelType = 8</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Reflected Light Aperture = 33.0550918196995</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Reflected Light Shutter = 2</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ReflectedLightFieldstop = 91.93324061196105</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Reflector = Brightfield Refl.light</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Reflector ID = Reflector.424928-9901-000</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Reflector Position = 1</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ReflectorMagnification = 1.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">RelFocusPosition1 0 = 0.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">RelFocusPosition2 0 = 0.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Factor for X = 1.2226807274950329</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Factor for Y = 1.2226807274950329</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Factor for Z = 1.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Height = 19456.51841662846</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Unit for X = 76</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Unit for Y = 76</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Unit for Z = 0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Scale Width = 13491.059147180193</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Stage Position X = 30007.16452132049</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Stage Position X 0 = 30007.16452132049</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Stage Position Y = -27872.242520632724</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Stage Position Y 0 = -27872.242520632724</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Stage calibrated = false</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">WhiteValue = 1.0</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">X position for position </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 30007.16452132049</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">X position for position </span></em><span class="hashtag"><i>#2</i></span><em><span style="font-family:"Helvetica",sans-serif"> = 30007.16452132049</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Y position for position </span></em><span class="hashtag"><i>#1</i></span><em><span style="font-family:"Helvetica",sans-serif"> = -27872.242520632724</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Y position for position </span></em><span class="hashtag"><i>#2</i></span><em><span style="font-family:"Helvetica",sans-serif"> = -27872.242520632724</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_2071 0 = 0.0_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_2298 = 49_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_5510 = 3.0_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_6122 = 2_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_6127 = 4_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_6128 = 7.3390625_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_65666 = 1.0_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_65669 = 0.0_<br>
<em><span style="font-family:"Helvetica",sans-serif">tag</span></em>ID_65681 = false_</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">--</span></em><span lang="EN-US" style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222"><br>
<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>
_ _<br>
<em><span style="font-family:"Helvetica",sans-serif">Title: RB152.1.2.11F</span></em>RB152.1.2.11D.zvi_<br>
<em><span style="font-family:"Helvetica",sans-serif">Width: 13491.0591 microns (11034)</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Height: 19456.5184 microns (15913)</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Size: 1005MB</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Resolution: 0.8179 pixels per micron</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Voxel size: 1.2227x1.2227x1 micron^3</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">ID: -11</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Bits per pixel: 16 (unsigned)</span></em><br>
<em><span style="font-family:"Helvetica",sans-serif">Display ranges</span></em><br>
_ 1: 0-65520_<br>
_ 2: 240-65520_<br>
_ 3: 0-65520_<br>
<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>
_ Channels: 3_<br>
_ Composite mode: "composite"_<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"><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"><a href="mailto:Alban.Favre@ggbearings.com">Alban.Favre@ggbearings.com</a></span><o:p></o:p></p>
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