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<div>Hi,</div>
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<div>You can check your Bio-Formats version by selecting,</div>
<div>Help—>About Plugins—> Bio-Formats Plugins…</div>
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<div>Or by running the following macro,</div>
<div>run("Bio-Formats Plugins...”);</div>
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<div>We will check the files and get back to you at the earliest.</div>
<div>Hope that helps.</div>
<div class="" style="font-family: Calibri; font-size: medium;"><br>
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<div class="" style="font-family: Calibri; font-size: medium;">Best,</div>
<div class="" style="font-family: Calibri; font-size: medium;">Balaji</div>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
<div style="color: rgb(40, 40, 40);">
<p>Mr Balaji Ramalingam</p>
<p>Software Developer<br>
</p>
<p>OME Team</p>
<p>College of Life Sciences</p>
<p>University of Dundee</p>
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</div>
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<span style="font-weight:bold">From: </span>Oliver Brookes <<a href="mailto:o.brookes@qmul.ac.uk">o.brookes@qmul.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 7 June 2016 17:13<br>
<span style="font-weight:bold">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] multi-scene .czi files<br>
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<p>Hi Sebastien,</p>
<p><br>
</p>
<p>I've uploaded one of my problem files. How do I check the bioformats version number please? I have the update site checked in the FIJI options, and I keep FIJI up to date, so I expect it to be the right version.<br>
<br>
The images don't open. It throws an error message very similar to the one reported by Michael Cammer on the OME list in march of this year. My error log contents are:<br>
<br>
</p>
<div>(Fiji Is Just) ImageJ 2.0.0-rc-49/1.51a; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 41MB of 6009MB (<1%)</div>
<div> </div>
<div>java.lang.NumberFormatException: null</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:542)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:615)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2268)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1329)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:731)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:140)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:76)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:216)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:180)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:137)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.run(Executer.java:66)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:745)</div>
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<p></p>
<p>Let me just clarify that this only happens on multi-position images. Normal images, stacks and videos open fine. When I hover the mouse over the files that won't open (in windows 7), or look at their properties, they all have XYCZTSB dimensions, but the
ones that will open all only have XYCZT. If I use the zen software to split the images into individual scenes, the scenes still retain the XYCZTSB, although S and B now always have a value of 1, and they still fail to open and throw the error message.</p>
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<p>Thanks for looking into this,</p>
<p><br>
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<p>Oliver</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri,sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Sebastien
Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk">s.besson@dundee.ac.uk</a>><br>
<b>Sent:</b> 06 June 2016 11:02:00<br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] multi-scene .czi files</font>
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</div>
<div>Hi Oliver,
<div class=""><br class="">
</div>
<div class="">the Zeiss scene dimension should be supported by Bio-Formats and we certainly have</div>
<div class="">several representative CZI datasets including multiple scenes tested daily.</div>
<div class=""><br class="">
</div>
<div class="">Could you first of all confirm you are using Bio-Formats 5.1.10 in Fiji? Also, can you give us</div>
<div class="">more detail about the issue: is an error thrown by Bio-Formats when opening the file or is a</div>
<div class="">single position opened with wrong dimensions? Finally do you have a sample file that you could</div>
<div class="">upload to <a href="http://qa.openmicroscopy.org.uk/qa/upload/" class="">
http://qa.openmicroscopy.org.uk/qa/upload/</a> to reproduce the issue?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 2 Jun 2016, at 10:25, Oliver Brookes <<a href="mailto:o.brookes@qmul.ac.uk" class="">o.brookes@qmul.ac.uk</a>> wrote:</div>
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<p class="">Hello, I've found that it's not possible to open multiple scene Zeiss images using bioformats in FIJI. Using the "positions" option on our Zeiss Elyra, it's possible to store multiple locations and automatically take pictures (very good for timelapse
video). The positional info is stored in the .czi format as a "scene" dimension - the dimensions of the file are listed as XYCZTSB. I can open czi images, stacks and movies that are taken at single positions (anything where the dimensions of the .czi file
are XYCZT). Is the extended .czi format not supported?</p>
<p class=""><br class="">
</p>
<p class="">Thanks,</p>
<p class=""><br class="">
</p>
<p class="">Oliver</p>
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