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Hi Darren,
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<div class="">If you convert the file to TIFF using bfconvert from the Bio-Formats command line tools do you still have the same issue?</div>
<div class=""><a href="https://www.openmicroscopy.org/bio-formats/downloads/" class="">https://www.openmicroscopy.org/bio-formats/downloads/</a></div>
<div class=""><a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/users/comlinetools/conversion.html" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/users/comlinetools/conversion.html</a> </div>
<div class=""><br class="">
</div>
<div class="">If you have one of the converted files showing the issue which is less than 2GB you can upload it to
<a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a> for us to test.</div>
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</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
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</div>
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<blockquote type="cite" class="">
<div class="">On 21 Jan 2019, at 16:18, Darren Thomson <<a href="mailto:darren.thomson@MANCHESTER.AC.UK" class="">darren.thomson@MANCHESTER.AC.UK</a>> wrote:</div>
<br class="Apple-interchange-newline">
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Hello All,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I am unable to import TIFF / OME.TIF into FIJI. I get the following errors upon going through Bioformats Importer.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I converted my .nd2 file in NIS into TIFF (since the nd2 was so large) for readability.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Can anyone help?<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Many thanks,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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CONSOLE:<o:p class=""></o:p></div>
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Warning: org.apache.xerces.parsers.SAXParser: Feature '<a href="http://javax.xml.xmlconstants/feature/secure-processing'" style="color: purple; text-decoration: underline;" class="">http://javax.xml.XMLConstants/feature/secure-processing'</a><span class="Apple-converted-space"> </span>is
not recognized.<o:p class=""></o:p></div>
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Warning: org.apache.xerces.parsers.SAXParser: Property '<a href="http://javax.xml.xmlconstants/property/accessExternalDTD'" style="color: purple; text-decoration: underline;" class="">http://javax.xml.XMLConstants/property/accessExternalDTD'</a><span class="Apple-converted-space"> </span>is
not recognized.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Warning: org.apache.xerces.parsers.SAXParser: Property '<a href="http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit'" style="color: purple; text-decoration: underline;" class="">http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit'</a><span class="Apple-converted-space"> </span>is
not recognized.<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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EXCEPTION:<o:p class=""></o:p></div>
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(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 110MB of 26000MB (<1%)<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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java.lang.ArithmeticException: / by zero<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:293)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:251)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:151)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:1181)<o:p class=""></o:p></div>
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at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p class=""></o:p></div>
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at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)<o:p class=""></o:p></div>
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at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)<o:p class=""></o:p></div>
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at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p class=""></o:p></div>
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at loci.plugins.in.Importer.run(Importer.java:76)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p class=""></o:p></div>
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at ij.IJ.runUserPlugIn(IJ.java:228)<o:p class=""></o:p></div>
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at ij.IJ.runPlugIn(IJ.java:192)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at ij.Executer.runCommand(Executer.java:137)<o:p class=""></o:p></div>
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at ij.Executer.run(Executer.java:66)<o:p class=""></o:p></div>
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at java.lang.Thread.run(Thread.java:745)<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class="">Dr Darren Thomson</b><span class=""><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span><span style="color: gray;" class="">Experimental Officer<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 22px;" class="">
<span style="color: gray;" class="">Manchester Fungal Infection Group<span class="Apple-converted-space"> </span></span><span class=""><a href="http://research.bmh.manchester.ac.uk/mfig" style="color: purple; text-decoration: underline;" class=""><span style="color: blue;" class="">(MFIG)</span></a><span style="color: gray;" class=""><o:p class=""></o:p></span></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: gray;" class="">Tel: (+44) (0)161 306 2457<o:p class=""></o:p></span></div>
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<span style="color: gray;" class="">Email:<span class="Apple-converted-space"> </span></span><span class=""><a href="mailto:darren.thomson@manchester.ac.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: blue;" class="">darren.thomson@manchester.ac.uk</span></a><u class=""><span style="color: gray;" class=""><o:p class=""></o:p></span></u></span></div>
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<span class=""><span id="cid:image001.png@01D4B1A4.F13BFBA0"><image001.png></span><o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 9pt; font-family: 'Segoe UI', sans-serif; color: rgb(148, 138, 84);" class="">Manchester Fungal Infection Group</span></b><span style="color: gray;" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 9pt; font-family: 'Segoe UI', sans-serif; color: rgb(148, 138, 84);" class="">NUS Gold Award Winners 2016 for Lab Sustainability<o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class="">Interested in studying Infection Biology?<span class="Apple-converted-space"> </span><a href="http://www.manchester.ac.uk/study/masters/courses/list/12079/mres-infection-biology/" style="color: purple; text-decoration: underline;" class=""><span style="color: blue;" class="">Click
here</span></a><o:p class=""></o:p></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span class=""><a href="https://www.rms.org.uk/study-read/news-listing-page/rms-digital-calendar-available-to-download.html" style="color: purple; text-decoration: underline;" class=""><span style="color: blue;" class="">Download the 2019 Royal
Microscopical Society digital calendar</span></a></span></b><b class=""><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 9pt; font-family: 'Segoe UI', sans-serif; color: rgb(148, 138, 84);" class=""> </span></b></div>
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<o:p class=""> </o:p></div>
</div>
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div>
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