<div dir="ltr">I will. Thank you.</div><div class="gmail_extra"><br clear="all"><div><br>--<br>HadiM</div>
<br><br><div class="gmail_quote">On Mon, Oct 28, 2013 at 6:56 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi HadiM,<br>
<div class="im"><br>
> I just updated bioformats toggling the Bio-Formats daily builds update site<br>
> and I can't reproduced the bug. But I have another one which prevent me to<br>
> open OME Tif from Micro Manager. Maybe the last one has been fixed or the<br>
> new one is raised before the last one, I can't tell.<br>
<br>
</div>...snipped error message...<br>
<div class="im"><br>
> Error message seems logic. Reader because as I said one channels contains<br>
> only one frame every ten so images count is not Z*C*T but Z*T+Z*T/10.<br>
><br>
> I attached an OME Tiff file to this mail.<br>
<br>
</div>For the acquisition that you describe, this OME-TIFF file is incorrect; this<br>
would need to be corrected in Micromanager.<br>
<br>
There are two ways to record acquisitions with holes in OME-TIFF:<br>
<br>
1) Store a blank plane for each of the non-recorded planes. This means<br>
that you would have Z * C * T planes in the file, but only Z * T + Z * T/10<br>
would be valid.<br>
<br>
2) Store each of the channels in a separate stack (i.e. OME Image). The<br>
first OME Image (representing channel 0) would contain Z * T planes; the<br>
second OME Image (representing channel 1) would contain Z * T / 10 planes.<br>
<br>
Simply omitting planes as is the case here is not currently supported. If you<br>
are already in contact with the Micromanager developers, then you may wish to<br>
pass this along; otherwise, let us know and we'll get in touch with them.<br>
<br>
Regards,<br>
-Melissa<br>
<div><div class="h5"><br>
On Sat, Oct 26, 2013 at 04:04:28PM +0200, HadiM wrote:<br>
> I just updated bioformats toggling the Bio-Formats daily builds update site<br>
> and I can't reproduced the bug. But I have another one which prevent me to<br>
> open OME Tif from Micro Manager. Maybe the last one has been fixed or the<br>
> new one is raised before the last one, I can't tell.<br>
><br>
> This is the new bug:<br>
><br>
> ```<br>
> (Fiji Is Just) ImageJ 1.48e; Java 1.7.0_25 [64-bit]; Linux<br>
> 3.11.0-12-generic; 31MB of 922MB (3%)<br>
><br>
> java.lang.IllegalArgumentException: ZCT size vs image count mismatch<br>
> (sizeZ=6, sizeC=1, sizeT=100, total=660)<br>
> at loci.formats.FormatTools.getIndex(FormatTools.java:355)<br>
> at loci.formats.FormatTools.getIndex(FormatTools.java:289)<br>
> at loci.formats.DimensionSwapper.getIndex(DimensionSwapper.java:277)<br>
> at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)<br>
> at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)<br>
> at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)<br>
> at loci.plugins.in.ImagePlusReader.getPlanesToLoad(ImagePlusReader.java:541)<br>
> at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:364)<br>
> at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)<br>
> at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)<br>
> at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)<br>
> at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)<br>
> at loci.plugins.in.Importer.readPixels(Importer.java:150)<br>
> at loci.plugins.in.Importer.run(Importer.java:89)<br>
> at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
> at ij.IJ.runUserPlugIn(IJ.java:196)<br>
> at ij.IJ.runPlugIn(IJ.java:160)<br>
> at ij.Executer.runCommand(Executer.java:131)<br>
> at ij.Executer.run(Executer.java:64)<br>
> at java.lang.Thread.run(Thread.java:724)<br>
> ```<br>
><br>
> Error message seems logic. Reader because as I said one channels contains<br>
> only one frame every ten so images count is not Z*C*T but Z*T+Z*T/10.<br>
><br>
> I attached an OME Tiff file to this mail.<br>
><br>
><br>
><br>
> --<br>
> HadiM<br>
><br>
><br>
> On Sat, Oct 26, 2013 at 3:36 PM, HadiM <<a href="mailto:marelo64@gmail.com">marelo64@gmail.com</a>> wrote:<br>
><br>
> > Hi,<br>
> ><br>
> > I have issues importing OME Tiff files created by Micro Manager (with<br>
> > oimave stack file option).<br>
> ><br>
> > This is the error message I have:<br>
> ><br>
> > (Fiji Is Just) ImageJ 1.48e; Java 1.7.0_25 [64-bit]; Linux 3.11.0-12-generic; 37MB of 1422MB (2%)<br>
> ><br>
> > java.lang.ArithmeticException: / by zero<br>
> > at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:277)<br>
> > at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:235)<br>
> > at loci.formats.MetadataTools.populatePixels(MetadataTools.java:136)<br>
> > at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:817)<br>
> > at loci.formats.FormatReader.setId(FormatReader.java:1244)<br>
> > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br>
> > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
> > at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br>
> > at loci.plugins.in.Importer.run(Importer.java:79)<br>
> > at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
> > at ij.IJ.runUserPlugIn(IJ.java:196)<br>
> > at ij.IJ.runPlugIn(IJ.java:160)<br>
> > at ij.Executer.runCommand(Executer.java:131)<br>
> > at ij.Executer.run(Executer.java:64)<br>
> > at java.lang.Thread.run(Thread.java:724)<br>
> ><br>
> > Last thing, Tiff files contains ome “holes”. In fact during acquisition I<br>
> > am imaging two channels and one of them is imaged every 6 frames. So for<br>
> > this channel there is an image only every 6 frames.<br>
> ><br>
> > I have the feeling that the issue is coming from there.<br>
> ><br>
> > MM can open the OME Tiff file correctly. I think this is because they have<br>
> > their own OME Tiff writer/reader.<br>
> ><br>
> > Any idea on how to fix this and when ?<br>
> ><br>
> > —<br>
> > HadiM<br>
> ><br>
<br>
<br>
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<br>
</blockquote></div><br></div>