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Hi Ofra,
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<div class="">Firstly, apologies for the delay in investigating this issue over the holidays and thank you for providing us with access to the data.</div>
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<div class="">I have been debugging the file-set over the past few days and have found the following:</div>
<div class="">- The specific error you had been seeing (loci.formats.FormatException: Unmatched UUID: urn:uuid:28c78877-7c97-4062-a4cc-f5d95b5e403a) relates to file for time-point 56 which it is unable to locate.</div>
<div class="">- The individual file for this time-point T56 appears to be correct with the expected UUID as above</div>
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<div class="">- The reason why it is looking for this file (along with the other related files) is due to the fact that each of the images for individual time-points contains metadata linking to the full dataset and the files will automatically act as a grouped
data-set</div>
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<div class="">If you wish to open these files individually in Fiji without it loading the entire dataset then you can use the option to open files individually. This can be set either through the Bio-Formats importer dialog or by the using the importer option
below:</div>
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<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">[ungroupFiles]</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">type = boolean</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">label = Open_files individually</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">info = <b>Open files individually</b> - \</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""> Treats each file as an individual file, instead of attempting to group \</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""> it together with other files that belong to a larger
<span style="text-decoration: underline" class="">dataset</span>.</div>
<div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">default = false</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 19 Dec 2016, at 15:50, Ofra Golani <<a href="mailto:ofra.golani@WEIZMANN.AC.IL" class="">ofra.golani@WEIZMANN.AC.IL</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Sebastien,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I couldn’t upload to your site<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I uploaded the files to our ftp site</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Please contact me personally for user+password<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Ofra<o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Sebastien Besson (Staff)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Friday, December 16, 2016 12:43 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>users OME<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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Hi Ofra,<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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the exception message you got below hints at a partial (or corrupter fileset). Would it be possible<o:p class=""></o:p></div>
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to upload the complete content of the test1 directory to <a href="http://qa.openmicroscopy.org.uk/qa/upload/" style="color: purple; text-decoration: underline;" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a> ?<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Best,<o:p class=""></o:p></div>
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Sebastien<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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On 15 Dec 2016, at 14:05, Ofra Golani <<a href="mailto:ofra.golani@weizmann.ac.il" style="color: purple; text-decoration: underline;" class="">ofra.golani@weizmann.ac.il</a>> wrote:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">HI,</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I enabled Java8 and disabled Bio-Formats update site, and repeated the export to ome.tif</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">When tied to open the files (from another computer) while they were created – the I could open independent ome files in Fiji (from another computer) and it looked
fine,</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">However, when the whole export wad done and I tried to open the independent files I had a problem:</span><o:p class=""></o:p></div>
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<span style="font-family: Calibri, sans-serif;" class=""><span class="">-<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span></span><span dir="LTR" class=""></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Dragging
1 file into Fiji – I got an error saying that “File is not in a supported format, a reader plugin is not available, or it was not found”<span class="Apple-converted-space"> </span></span><o:p class=""></o:p></div>
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<span style="font-family: Calibri, sans-serif;" class=""><span class="">-<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span></span><span dir="LTR" class=""></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Trying
to open one file with Bio-Format Importer I got an exception</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">loci.formats.FormatException: Unmatched UUID: urn:uuid:28c78877-7c97-4062-a4cc-f5d95b5e403a</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:617)</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.formats.FormatReader.setId(FormatReader.java:1399)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.plugins.in.Importer.showDialogs(Importer.java:140)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.plugins.in.Importer.run(Importer.java:76)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at loci.plugins.LociImporter.run(LociImporter.java:78)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at ij.IJ.runUserPlugIn(IJ.java:217)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at ij.IJ.runPlugIn(IJ.java:181)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at ij.Executer.runCommand(Executer.java:137)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at ij.Executer.run(Executer.java:66)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 1in; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> at java.lang.Thread.run(Thread.java:745)</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -0.25in;" class="">
<span style="font-family: Calibri, sans-serif;" class=""><span class="">-<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span></span><span dir="LTR" class=""></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Tring
to open 1 file from a folder where all the Time-points files are saved , opens a hyperstack of all the files , although I didn’t ask to group files:</span><o:p class=""></o:p></div>
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<span style="font-family: Calibri, sans-serif;" class=""><span class="">-<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span></span><span dir="LTR" class=""></span><image001.png><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The above is the choices I made, and here is the recorded command</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">run("Bio-Formats Importer", "open=[D:<a href="smb://UserData/innaa/test" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\test</a><span class="Apple-converted-space"> </span>fiji\\test1\\test1_T17.ome.tif]
autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Please advise</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Ofra</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Sebastien Besson (Staff)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, December 14, 2016 3:36 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>users OME<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file</span><o:p class=""></o:p></div>
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HI Ofra,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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the issue below also reported in a screenshot in your previous email matches what was<o:p class=""></o:p></div>
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reported a few days ago [1].<o:p class=""></o:p></div>
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Which update sites do you have enabled? In particular is the Bio-Formats update site [2]<o:p class=""></o:p></div>
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enabled? If so, could you disable it (the Java 8 update site should ship Bio-Formats 5.3.0)<o:p class=""></o:p></div>
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and test whether this solves this export problem?<o:p class=""></o:p></div>
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Best,<o:p class=""></o:p></div>
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Sebastien<o:p class=""></o:p></div>
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[1] <a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html" style="color: purple; text-decoration: underline;" class="">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html</a> <o:p class=""></o:p></div>
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[2] <a href="http://imagej.net/Bio-Formats#Daily_builds" style="color: purple; text-decoration: underline;" class="">http://imagej.net/Bio-Formats#Daily_builds</a><o:p class=""></o:p></div>
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On 14 Dec 2016, at 12:19, Ofra Golani <<a href="mailto:ofra.golani@weizmann.ac.il" style="color: purple; text-decoration: underline;" class="">ofra.golani@weizmann.ac.il</a>> wrote:<o:p class=""></o:p></div>
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Hi,<br class="">
<br class="">
Following on the same problem<br class="">
<br class="">
When saving working with big files there is another problem when using Bio-Formats Exporter to save individual time-points into separate ome.tif files.<br class="">
I'll upload the file for you to our ftp server, please write me privately and I'll send you the download instructions.<span class="Apple-converted-space"> </span><br class="">
It's a 75 GB file<br class="">
<br class="">
Note that this time virtual-stack is used, The recorded command is:<span class="Apple-converted-space"> </span><br class="">
<br class="">
run("Bio-Formats Exporter", "save=[D:<a href="smb://UserData/innaa/test" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\test</a><span class="Apple-converted-space"> </span>fiji\\test.ome.tif] write_each_timepoint export compression=Uncompressed
color_mode=Default quiet rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT color_mode=Default quiet rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack");<br class="">
<br class="">
The generated ome.tif files cannot be opened with Bio-Formats importer and lead to Exception<span class="Apple-converted-space"> </span><br class="">
<br class="">
(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Windows Server 2012 R2 6.3; 75376MB of 196255MB (38%)<br class="">
<br class="">
java.lang.NoClassDefFoundError: ome/xml/meta/MetadataConverter<br class="">
at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:876)<br class="">
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:554)<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1399)<br class="">
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<br class="">
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<br class="">
at loci.plugins.in.Importer.showDialogs(Importer.java:140)<br class="">
at loci.plugins.in.Importer.run(Importer.java:76)<br class="">
at loci.plugins.LociImporter.run(LociImporter.java:78)<br class="">
at ij.IJ.runUserPlugIn(IJ.java:217)<br class="">
at ij.IJ.runPlugIn(IJ.java:181)<br class="">
at ij.IJ.runPlugIn(IJ.java:170)<br class="">
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)<br class="">
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)<br class="">
at ij.IJ.runUserPlugIn(IJ.java:217)<br class="">
at ij.IJ.runPlugIn(IJ.java:181)<br class="">
at ij.IJ.runPlugIn(IJ.java:170)<br class="">
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)<br class="">
at ij.io.Opener.openImage(Opener.java:369)<br class="">
at ij.io.Opener.openImage(Opener.java:243)<br class="">
at ij.io.Opener.open(Opener.java:110)<br class="">
at ij.io.Opener.openAndAddToRecent(Opener.java:292)<br class="">
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)<br class="">
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)<br class="">
at java.lang.Thread.run(Thread.java:745)<br class="">
<br class="">
<br class="">
Best<br class="">
Ofra<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
________________________________________<br class="">
From: ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>] on behalf of Ofra Golani [<a href="mailto:ofra.golani@weizmann.ac.il" style="color: purple; text-decoration: underline;" class="">ofra.golani@weizmann.ac.il</a>]<br class="">
Sent: Wednesday, December 14, 2016 10:10 AM<br class="">
To: OME User Support List<br class="">
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file<br class="">
<br class="">
Hi,<br class="">
<br class="">
Thanks for looking into this.<br class="">
I tried to reproduce the problem and it is different from what I wrote before.<br class="">
<br class="">
In Summary:<br class="">
1. separating into different ome.tif files for each time points - works OK<br class="">
2. separating into different tif files for each time points - produce file with corrupted pixel values (only first slice is OK)<br class="">
3. saving hyperstack into one ome.tif produce file which is missing one image and cannot be rearranged into hyperstack correctly.<br class="">
4. saving hyperstack into one tif produce file of the correct size but with corrupted pixel values (only first slice is OK)<br class="">
5. saving hyperstack into one tif with regular Fiji Save As tif works fine<br class="">
<br class="">
I uploaded sample files for you into my box folder:<span class="Apple-converted-space"> </span><a href="https://weizmann.box.com/s/xhbixjp0ydbd5qd69s2xnm9k2lugvdri" style="color: purple; text-decoration: underline;" class="">https://weizmann.box.com/s/xhbixjp0ydbd5qd69s2xnm9k2lugvdri</a><br class="">
It also reproduced with the Mitosis sample file<br class="">
<br class="">
See details below<br class="">
<br class="">
Best Regards<br class="">
Ofra<br class="">
<br class="">
<br class="">
Details:<br class="">
=====<br class="">
<br class="">
<br class="">
BioFormats version: 5.3.0-SNAPSHOT, Build Date: 9 decemebr 2016<br class="">
<br class="">
Here is my recorded command when saving in tif format<br class="">
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/Mitosis/mito1.tif" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito1.tif</a><span class="Apple-converted-space"> </span>write_each_timepoint
compression=Uncompressed");<br class="">
<br class="">
I opened the file of the first time-point ("mito1_T0.tif")<br class="">
Attached are snapshots comparing the slices to the original slices and the corrupted file itself<br class="">
<br class="">
Here is the recorded command for saving in ome.tif format<br class="">
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/Mitosis/mito2.ome.tif" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito2.ome.tif</a>write_each_timepoint
compression=Uncompressed");<br class="">
<br class="">
When I try to open it by drag and drop the file ("mito2_T0.ome.tif") is opened as stack instead of hyperstack , after reorganizing it, it looks OK (Can't reproduce the corruption).<br class="">
When I try to open it with BioFormats Importer I get an exception (attached)<br class="">
<br class="">
The same behavior reproduced on my workstation (Windows7, which has Release 5.3.0-SNAPSHOT build date 5 December 2016, see attachment)<br class="">
<br class="">
My original problem is with much bigger czi file (3D+time) that I try to crop and output to different files for different time-points.<br class="">
<br class="">
I crop part of the big file (95 GB) so that I have now 16 slices * 11 time points<br class="">
<br class="">
- exporting (on the WindowsServer WS) to ome.tif produces a file with only 175 images so 1 image is missing and I cannot rearrange it into hyperstack:<br class="">
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/AllTP.ome.tif" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP.ome.tif</a>compression=Uncompressed");<br class="">
<br class="">
- exporting into into one tif file produces hyperstack of the correct size, but with corrupted pixel values<br class="">
<br class="">
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/AllTP.tif" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP.tif</a>compression=Uncompressed");<br class="">
<br class="">
- Saving the file using the regular Fiji Save As Tif option produces a hyperstack of the real size with the original pixel values - You can use it as a starting point for reproducing the problems<br class="">
<br class="">
saveAs("Tiff", "D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP_SaveAsTif.tif");<br class="">
<br class="">
<br class="">
However - I need to separate into independent file for each time point. So when using BioFormat Exporter to save each independent TP into file with<br class="">
<br class="">
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/SepTP.ome.tif" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.ome.tif</a><span class="Apple-converted-space"> </span>write_each_timepoint
compression=Uncompressed");<br class="">
<br class="">
produce valid stacks - so no problem here<br class="">
<br class="">
When writing into tif the output files have corrupted pixel values<br class="">
<br class="">
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/SepTP.tif" style="color: purple; text-decoration: underline;" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.tif</a><span class="Apple-converted-space"> </span>write_each_timepoint
compression=Uncompressed");<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
-----Original Message-----<br class="">
From: ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>] On Behalf Of Balaji Ramalingam (Staff)<br class="">
Sent: Tuesday, December 13, 2016 5:56 PM<br class="">
To: OME User Support List<br class="">
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file<br class="">
<br class="">
Hi Ofra,<br class="">
<br class="">
Thank you for reporting your issue.<br class="">
Testing the same locally, we were unfortunately unable to reproduce the bug.<br class="">
<br class="">
I have recorded the Fiji/ImageJ operations that I had performed (using the Fiji/ImageJ macro recorder) and I have pasted the same here,<br class="">
<br class="">
run("Bio-Formats Exporter",<br class="">
"save=/Users/bramalingam/Desktop/FijiExportTest/mitosisOmeTiff/mitosis_time<br class="">
point_.ome.tif write_each_timepoint compression=Uncompressed²);<br class="">
<br class="">
I reimported the resultant images back into Fiji/ImageJ and compared the pixel data with the original image.<br class="">
<br class="">
There was no obvious issue that was noticed, thus could you please record your mouse-click operations via the Fiji/ImageJ macro recorder and paste the resultant command here? The documentation for the same can be found here,<a href="https://imagej.net/Introduction_into_Macro_Programming#The_recorder" style="color: purple; text-decoration: underline;" class="">https://imagej.net/Introduction_into_Macro_Programming#The_recorder</a><br class="">
<br class="">
<br class="">
And also it would be great if you could clarify the version of Bio-Formats that was used? (I have updated my Fiji to use the latest release version of Bio-Formats : Version 5.3.0)<br class="">
<br class="">
You can get the same by selecting,<br class="">
Help‹>About Plugins‹>Bio-Formats PluginsŠ (in the Fiji menu)<br class="">
<br class="">
Or by running the following macro command, run("Bio-Formats Plugins...²);<br class="">
<br class="">
This would help us troubleshoot the issue in better detail.<br class="">
<br class="">
Best,<br class="">
Balaji<br class="">
<br class="">
<br class="">
__________________<br class="">
Mr Balaji Ramalingam<br class="">
Software Developer<br class="">
<br class="">
OME Team<br class="">
School of Life Sciences<br class="">
University of Dundee<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 12/12/2016, 14:54, "ome-users on behalf of Ofra Golani"<br class="">
<<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a><span class="Apple-converted-space"> </span>on behalf of<span class="Apple-converted-space"> </span><a href="mailto:ofra.golani@weizmann.ac.il" style="color: purple; text-decoration: underline;" class="">ofra.golani@weizmann.ac.il</a>>
wrote:<br class="">
<br class="">
<br class="">
<br class="">
<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Hi,<br class="">
<br class="">
I encounter a problem when using Bio-Formats exporter to save each<br class="">
time-point into separate file.<br class="">
It saves into separate files, but the files are corrupted. You see this<br class="">
when you move through the slices.<br class="">
You can try this with the "Mitosis" 5D stack of Fiji Sample files.<br class="">
The problem happens when I save files both as tif and as ome.tif.<br class="">
I use the latest Fiji version, with the latest Bio-Formats version.<br class="">
<br class="">
Please advise,<br class="">
Thanks,<br class="">
<br class="">
Ofra<br class="">
<br class="">
----------------------------------------<br class="">
<br class="">
Ofra Golani<br class="">
<br class="">
BioImage Analyst<br class="">
Life Sciences Core Facilities<br class="">
Weizmann Institute of Science<br class="">
Tel: +972-8-934-5177<br class="">
<a href="mailto:ofra.golani@weizmann.ac.il" style="color: purple; text-decoration: underline;" class="">ofra.golani@weizmann.ac.il</a><br class="">
<a href="http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/ab" style="color: purple; text-decoration: underline;" class="">http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/ab</a><br class="">
out<br class="">
-service<br class="">
<br class="">
<br class="">
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