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Hi Oliver,
<div class=""><br class="">
</div>
<div class="">thanks for following up on this thread. The error you reported is expected as we did not</div>
<div class="">get this work finalized in time for Bio-Formats 5.2.0.</div>
<div class=""><br class="">
</div>
<div class="">However, the bug fix for this CZI issues will be included in Bio-Formats 5.2.1 which we</div>
<div class="">expect to release on Thursday.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 23 Aug 2016, at 11:50, Oliver Brookes <<a href="mailto:o.brookes@qmul.ac.uk" class="">o.brookes@qmul.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<p class="">Hi Sebastien,</p>
<p class=""><br class="">
</p>
<p class="">I've just updated to bioformats 5.2 in FIJI, but I'm still not able to open these .czi files. Error log looks pretty similar to before:<br class="">
<br class="">
</p>
<div class="">(Fiji Is Just) ImageJ 2.0.0-rc-49/1.51f; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 33MB of 6009MB (<1%)</div>
<div class=""> </div>
<div class="">java.lang.NumberFormatException: null</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:542)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:615)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2489)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1550)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:913)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1401)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:140)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:76)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:217)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:181)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:137)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.run(Executer.java:66)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:745)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Any word on when this might be fixed?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Oliver</div>
<div class=""><br class="">
</div>
<br class="">
<div class=""><br class="webkit-block-placeholder">
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size:11pt" class=""><b class="">From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
 on behalf of Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>><br class="">
<b class="">Sent:</b> 10 June 2016 23:29:14<br class="">
<b class="">To:</b> users OME<br class="">
<b class="">Subject:</b> Re: [ome-users] multi-scene .czi files</font>
<div class=""> </div>
</div>
<div class="">Hi Oliver,
<div class=""><br class="">
</div>
<div class="">we are currently working on finalising our model and API changes.</div>
<div class="">The current plan is to have 5.2.0 released by the end of the Summer.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 8 Jun 2016, at 14:31, Oliver Brookes <<a href="mailto:o.brookes@qmul.ac.uk" class="">o.brookes@qmul.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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<p class="">Excellent, thanks for that. When is v5.2 likely to be released?</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size:11pt" class=""><b class="">From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
 on behalf of Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>><br class="">
<b class="">Sent:</b> 08 June 2016 08:55:52<br class="">
<b class="">To:</b> users OME<br class="">
<b class="">Subject:</b> Re: [ome-users] multi-scene .czi files</font>
<div class=""> </div>
</div>
<div class="">Hi Oliver,
<div class=""><br class="">
</div>
<div class="">I can certainly reproduce your issue using Bio-Formats 5.1.10 and the file you</div>
<div class="">uploaded.</div>
<div class=""><br class="">
</div>
<div class="">Note that a similar error to the one you described below has been reported in</div>
<div class=""><a href="https://github.com/openmicroscopy/bioformats/issues/2431" class="">https://github.com/openmicroscopy/bioformats/issues/2431</a> and we have a</div>
<div class="">bug fix proposed in <a href="https://github.com/openmicroscopy/bioformats/pull/2437" class="">https://github.com/openmicroscopy/bioformats/pull/2437</a> to</div>
<div class="">address it. </div>
<div class=""><br class="">
</div>
<div class="">We will make sure your uploaded file is included as well for the testing of the</div>
<div class="">Pull Request. I would expect the bug fix to be released with Bio-Formats 5.2.0.</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 7 Jun 2016, at 17:51, Balaji Ramalingam (Staff) <<a href="mailto:b.ramalingam@dundee.ac.uk" class="">b.ramalingam@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class="">
<div class="">
<div class="">Hi,</div>
<div class=""><br class="">
</div>
<div class="">You can check your Bio-Formats version by selecting,</div>
<div class="">Help—>About Plugins—> Bio-Formats Plugins…</div>
<div class=""><br class="">
</div>
<div class="">Or by running the following macro,</div>
<div class="">run("Bio-Formats Plugins...”);</div>
<div class=""><br class="">
</div>
<div class="">We will check the files and get back to you at the earliest.</div>
<div class="">Hope that helps.</div>
<div class="" style="font-family: Calibri; font-size: 12px;"><br class="">
</div>
<div class="" style="font-family: Calibri; font-size: 12px;">Best,</div>
<div class="" style="font-family: Calibri; font-size: 12px;">Balaji</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">
<div style="color: rgb(40, 40, 40);" class=""><span style="background-color: rgb(255, 255, 255);" class="">__________________</span></div>
<div style="color: rgb(40, 40, 40);" class="">
<p class="">Mr Balaji Ramalingam</p>
<p class="">Software Developer<br class="">
</p>
<p class="">OME Team</p>
<p class="">College of Life Sciences</p>
<p class="">University of Dundee</p>
</div>
</div>
</div>
</div>
<div class=""><br class="">
</div>
<span id="OLK_SRC_BODY_SECTION" class="">
<div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);" class="">
<span style="font-weight:bold" class="">From: </span>Oliver Brookes <<a href="mailto:o.brookes@qmul.ac.uk" class="">o.brookes@qmul.ac.uk</a>><br class="">
<span style="font-weight:bold" class="">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Tuesday, 7 June 2016 17:13<br class="">
<span style="font-weight:bold" class="">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [ome-users] multi-scene .czi files<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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<p class="">Hi Sebastien,</p>
<p class=""><br class="">
</p>
<p class="">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 class="">
<br class="">
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 class="">
<br class="">
</p>
<div class="">(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 class=""> </div>
<div class="">java.lang.NumberFormatException: null</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:542)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:615)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2268)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1329)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:731)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:140)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:76)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:216)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:180)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:137)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.run(Executer.java:66)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:745)</div>
<div class=""><br class="">
</div>
<br class="">
<div class=""><br class="webkit-block-placeholder">
</div>
<p class="">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>
<p class=""><br class="">
</p>
<p class="">Thanks for looking into this,</p>
<p class=""><br class="">
</p>
<p class="">Oliver</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri,sans-serif" style="font-size:11pt" class=""><b class="">From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
 on behalf of Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>><br class="">
<b class="">Sent:</b> 06 June 2016 11:02:00<br class="">
<b class="">To:</b> users OME<br class="">
<b class="">Subject:</b> Re: [ome-users] multi-scene .czi files</font>
<div class=""> </div>
</div>
<div class="">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 class="">
<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>
<br class="Apple-interchange-newline">
<div class=""><style type="text/css" style="display:none;" class=""><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div dir="ltr" class="">
<div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class="">
<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>
</div>
</div>
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</blockquote>
</div>
<br class="">
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<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
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</span><br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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ome-users mailing list<br class="">
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</blockquote>
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<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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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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