<div dir="ltr">I just updated bioformats toggling the Bio-Formats daily builds update site and I can't reproduced the bug. But I have another one which prevent me to open OME Tif from Micro Manager. Maybe the last one has been fixed or the new one is raised before the last one, I can't tell.<div>
<br></div><div>This is the new bug:</div><div><br></div><div>```</div><div><div>(Fiji Is Just) ImageJ 1.48e; Java 1.7.0_25 [64-bit]; Linux 3.11.0-12-generic; 31MB of 922MB (3%)</div><div> </div><div>java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=6, sizeC=1, sizeT=100, total=660)</div>
<div>at loci.formats.FormatTools.getIndex(FormatTools.java:355)</div><div>at loci.formats.FormatTools.getIndex(FormatTools.java:289)</div><div>at loci.formats.DimensionSwapper.getIndex(DimensionSwapper.java:277)</div><div>
at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)</div><div>at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)</div><div>at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)</div><div>at loci.plugins.in.ImagePlusReader.getPlanesToLoad(ImagePlusReader.java:541)</div>
<div>at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:364)</div><div>at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)</div><div>at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)</div>
<div>at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)</div><div>at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)</div><div>at loci.plugins.in.Importer.readPixels(Importer.java:150)</div>
<div>at loci.plugins.in.Importer.run(Importer.java:89)</div><div>at loci.plugins.LociImporter.run(LociImporter.java:81)</div><div>at ij.IJ.runUserPlugIn(IJ.java:196)</div><div>at ij.IJ.runPlugIn(IJ.java:160)</div><div>at ij.Executer.runCommand(Executer.java:131)</div>
<div>at ij.Executer.run(Executer.java:64)</div><div>at java.lang.Thread.run(Thread.java:724)</div></div><div>```</div><div><br></div><div>Error message seems logic. Reader because as I said one channels contains only one frame every ten so images count is not Z*C*T but Z*T+Z*T/10.</div>
<div><br></div><div>I attached an OME Tiff file to this mail.</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><br>--<br>HadiM</div>
<br><br><div class="gmail_quote">On Sat, Oct 26, 2013 at 3:36 PM, HadiM <span dir="ltr"><<a href="mailto:marelo64@gmail.com" target="_blank">marelo64@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div style="line-height:1.2;color:rgb(34,34,34);font-size:1em;font-family:Helvetica,arial,freesans,clean,sans-serif;border:none">
<p style="margin:1em 0px">Hi,</p>
<p style="margin:1em 0px">I have issues importing OME Tiff files created by Micro Manager (with oimave stack file option).</p>
<p style="margin:1em 0px">This is the error message I have:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;overflow:auto;margin:1em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:nowrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;white-space:pre-wrap;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block;padding:0.5em;color:rgb(51,51,51);background-color:rgb(248,248,255);background-repeat:initial initial">(Fiji Is Just) ImageJ 1.48e; Java 1.7.0_25 [64-bit]; Linux 3.11.0-12-generic; 37MB of 1422MB (2%)
java.lang.ArithmeticException: / by zero
at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:277)
at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:235)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:136)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:817)
at loci.formats.FormatReader.setId(FormatReader.java:1244)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:196)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:724)</code></pre>
<p style="margin:1em 0px">Last thing, Tiff files contains ome “holes”. In fact during acquisition I am imaging two channels and one of them is imaged every 6 frames. So for this channel there is an image only every 6 frames.</p>
<p style="margin:1em 0px">I have the feeling that the issue is coming from there.</p>
<p style="margin:1em 0px">MM can open the OME Tiff file correctly. I think this is because they have their own OME Tiff writer/reader.</p>
<p style="margin:1em 0px">Any idea on how to fix this and when ?</p>
<p style="margin:1em 0px">—<span class="HOEnZb"><font color="#888888"><br>HadiM </font></span></p>
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</blockquote></div><br></div>