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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Sebastien,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I couldn’t upload to your site
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I uploaded the files to our ftp site</span>
<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Please contact me personally for user+password<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ofra<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>Sebastien Besson (Staff)<br>
<b>Sent:</b> Friday, December 16, 2016 12:43 PM<br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Ofra, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">the exception message you got below hints at a partial (or corrupter fileset). Would it be possible<o:p></o:p></p>
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<p class="MsoNormal">to upload the complete content of the test1 directory to <a href="http://qa.openmicroscopy.org.uk/qa/upload/">http://qa.openmicroscopy.org.uk/qa/upload/</a> ?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">Sebastien<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On 15 Dec 2016, at 14:05, Ofra Golani <<a href="mailto:ofra.golani@weizmann.ac.il">ofra.golani@weizmann.ac.il</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">HI,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I enabled Java8 and disabled Bio-Formats update site, and repeated the export to ome.tif</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">However, when the whole export wad done and I tried to open the independent files I had a problem:</span><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-family:"Calibri","sans-serif""><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span dir="LTR"></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-family:"Calibri","sans-serif""><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span dir="LTR"></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Trying to open one file with Bio-Format Importer I got an exception
</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">loci.formats.FormatException: Unmatched UUID: urn:uuid:28c78877-7c97-4062-a4cc-f5d95b5e403a</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:617)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.formats.FormatReader.setId(FormatReader.java:1399)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.plugins.in.Importer.showDialogs(Importer.java:140)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.plugins.in.Importer.run(Importer.java:76)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at loci.plugins.LociImporter.run(LociImporter.java:78)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at ij.IJ.runUserPlugIn(IJ.java:217)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at ij.IJ.runPlugIn(IJ.java:181)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at ij.Executer.runCommand(Executer.java:137)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at ij.Executer.run(Executer.java:66)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> at java.lang.Thread.run(Thread.java:745)</span><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-family:"Calibri","sans-serif""><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span dir="LTR"></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="font-family:"Calibri","sans-serif""><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span dir="LTR"></span><image001.png><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.25in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The above is the choices I made, and here is the recorded command</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">run("Bio-Formats Importer", "open=[D:<a href="smb://UserData/innaa/test">\\UserData\\innaa\\test</a> fiji\\test1\\test1_T17.ome.tif]
autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.25in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.25in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Please advise</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.25in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.25in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ofra</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.25in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>Sebastien Besson (Staff)<br>
<b>Sent:</b> Wednesday, December 14, 2016 3:36 PM<br>
<b>To:</b> users OME<br>
<b>Subject:</b> Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file</span><o:p></o:p></p>
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</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">HI Ofra, <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">the issue below also reported in a screenshot in your previous email matches what was<o:p></o:p></p>
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<div>
<p class="MsoNormal">reported a few days ago [1].<o:p></o:p></p>
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<div>
<p class="MsoNormal">Which update sites do you have enabled? In particular is the Bio-Formats update site [2]<o:p></o:p></p>
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<p class="MsoNormal">enabled? If so, could you disable it (the Java 8 update site should ship Bio-Formats 5.3.0)<o:p></o:p></p>
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<p class="MsoNormal">and test whether this solves this export problem?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Sebastien<o:p></o:p></p>
</div>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">[1] <a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html</a> <o:p></o:p></p>
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<p class="MsoNormal">[2] <a href="http://imagej.net/Bio-Formats#Daily_builds">http://imagej.net/Bio-Formats#Daily_builds</a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On 14 Dec 2016, at 12:19, Ofra Golani <<a href="mailto:ofra.golani@weizmann.ac.il">ofra.golani@weizmann.ac.il</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi,<br>
<br>
Following on the same problem<br>
<br>
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>
I'll upload the file for you to our ftp server, please write me privately and I'll send you the download instructions.
<br>
It's a 75 GB file<br>
<br>
Note that this time virtual-stack is used, The recorded command is: <br>
<br>
run("Bio-Formats Exporter", "save=[D:<a href="smb://UserData/innaa/test">\\UserData\\innaa\\test</a> 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>
<br>
The generated ome.tif files cannot be opened with Bio-Formats importer and lead to Exception
<br>
<br>
(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>
<br>
java.lang.NoClassDefFoundError: ome/xml/meta/MetadataConverter<br>
at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:876)<br>
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:554)<br>
at loci.formats.FormatReader.setId(FormatReader.java:1399)<br>
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<br>
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<br>
at loci.plugins.in.Importer.showDialogs(Importer.java:140)<br>
at loci.plugins.in.Importer.run(Importer.java:76)<br>
at loci.plugins.LociImporter.run(LociImporter.java:78)<br>
at ij.IJ.runUserPlugIn(IJ.java:217)<br>
at ij.IJ.runPlugIn(IJ.java:181)<br>
at ij.IJ.runPlugIn(IJ.java:170)<br>
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)<br>
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)<br>
at ij.IJ.runUserPlugIn(IJ.java:217)<br>
at ij.IJ.runPlugIn(IJ.java:181)<br>
at ij.IJ.runPlugIn(IJ.java:170)<br>
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)<br>
at ij.io.Opener.openImage(Opener.java:369)<br>
at ij.io.Opener.openImage(Opener.java:243)<br>
at ij.io.Opener.open(Opener.java:110)<br>
at ij.io.Opener.openAndAddToRecent(Opener.java:292)<br>
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)<br>
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)<br>
at java.lang.Thread.run(Thread.java:745)<br>
<br>
<br>
Best<br>
Ofra<br>
<br>
<br>
<br>
<br>
________________________________________<br>
From: ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>] on behalf of Ofra Golani [<a href="mailto:ofra.golani@weizmann.ac.il">ofra.golani@weizmann.ac.il</a>]<br>
Sent: Wednesday, December 14, 2016 10:10 AM<br>
To: OME User Support List<br>
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file<br>
<br>
Hi,<br>
<br>
Thanks for looking into this.<br>
I tried to reproduce the problem and it is different from what I wrote before.<br>
<br>
In Summary:<br>
1. separating into different ome.tif files for each time points - works OK<br>
2. separating into different tif files for each time points - produce file with corrupted pixel values (only first slice is OK)<br>
3. saving hyperstack into one ome.tif produce file which is missing one image and cannot be rearranged into hyperstack correctly.<br>
4. saving hyperstack into one tif produce file of the correct size but with corrupted pixel values (only first slice is OK)<br>
5. saving hyperstack into one tif with regular Fiji Save As tif works fine<br>
<br>
I uploaded sample files for you into my box folder: <a href="https://weizmann.box.com/s/xhbixjp0ydbd5qd69s2xnm9k2lugvdri">
https://weizmann.box.com/s/xhbixjp0ydbd5qd69s2xnm9k2lugvdri</a><br>
It also reproduced with the Mitosis sample file<br>
<br>
See details below<br>
<br>
Best Regards<br>
Ofra<br>
<br>
<br>
Details:<br>
=====<br>
<br>
<br>
BioFormats version: 5.3.0-SNAPSHOT, Build Date: 9 decemebr 2016<br>
<br>
Here is my recorded command when saving in tif format<br>
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/Mitosis/mito1.tif">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito1.tif</a> write_each_timepoint compression=Uncompressed");<br>
<br>
I opened the file of the first time-point ("mito1_T0.tif")<br>
Attached are snapshots comparing the slices to the original slices and the corrupted file itself<br>
<br>
Here is the recorded command for saving in ome.tif format<br>
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/Mitosis/mito2.ome.tif">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito2.ome.tif</a> write_each_timepoint compression=Uncompressed");<br>
<br>
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>
When I try to open it with BioFormats Importer I get an exception (attached)<br>
<br>
The same behavior reproduced on my workstation (Windows7, which has Release 5.3.0-SNAPSHOT build date 5 December 2016, see attachment)<br>
<br>
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>
<br>
I crop part of the big file (95 GB) so that I have now 16 slices * 11 time points<br>
<br>
- 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>
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/AllTP.ome.tif">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP.ome.tif</a> compression=Uncompressed");<br>
<br>
- exporting into into one tif file produces hyperstack of the correct size, but with corrupted pixel values<br>
<br>
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/AllTP.tif">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP.tif</a> compression=Uncompressed");<br>
<br>
- 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>
<br>
saveAs("Tiff", "D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP_SaveAsTif.tif");<br>
<br>
<br>
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>
<br>
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/SepTP.ome.tif">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.ome.tif</a> write_each_timepoint compression=Uncompressed");<br>
<br>
produce valid stacks - so no problem here<br>
<br>
When writing into tif the output files have corrupted pixel values<br>
<br>
run("Bio-Formats Exporter", "save=D:<a href="smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/SepTP.tif">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.tif</a> write_each_timepoint compression=Uncompressed");<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
-----Original Message-----<br>
From: ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>] On Behalf Of Balaji Ramalingam (Staff)<br>
Sent: Tuesday, December 13, 2016 5:56 PM<br>
To: OME User Support List<br>
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file<br>
<br>
Hi Ofra,<br>
<br>
Thank you for reporting your issue.<br>
Testing the same locally, we were unfortunately unable to reproduce the bug.<br>
<br>
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>
<br>
run("Bio-Formats Exporter",<br>
"save=/Users/bramalingam/Desktop/FijiExportTest/mitosisOmeTiff/mitosis_time<br>
point_.ome.tif write_each_timepoint compression=Uncompressed²);<br>
<br>
I reimported the resultant images back into Fiji/ImageJ and compared the pixel data with the original image.<br>
<br>
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">https://imagej.net/Introduction_into_Macro_Programming#The_recorder</a><br>
<br>
<br>
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>
<br>
You can get the same by selecting,<br>
Help‹>About Plugins‹>Bio-Formats PluginsŠ (in the Fiji menu)<br>
<br>
Or by running the following macro command, run("Bio-Formats Plugins...²);<br>
<br>
This would help us troubleshoot the issue in better detail.<br>
<br>
Best,<br>
Balaji<br>
<br>
<br>
__________________<br>
Mr Balaji Ramalingam<br>
Software Developer<br>
<br>
OME Team<br>
School of Life Sciences<br>
University of Dundee<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 12/12/2016, 14:54, "ome-users on behalf of Ofra Golani"<br>
<<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of
<a href="mailto:ofra.golani@weizmann.ac.il">ofra.golani@weizmann.ac.il</a>> wrote:<br>
<br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">Hi,<br>
<br>
I encounter a problem when using Bio-Formats exporter to save each<br>
time-point into separate file.<br>
It saves into separate files, but the files are corrupted. You see this<br>
when you move through the slices.<br>
You can try this with the "Mitosis" 5D stack of Fiji Sample files.<br>
The problem happens when I save files both as tif and as ome.tif.<br>
I use the latest Fiji version, with the latest Bio-Formats version.<br>
<br>
Please advise,<br>
Thanks,<br>
<br>
Ofra<br>
<br>
----------------------------------------<br>
<br>
Ofra Golani<br>
<br>
BioImage Analyst<br>
Life Sciences Core Facilities<br>
Weizmann Institute of Science<br>
Tel: +972-8-934-5177<br>
<a href="mailto:ofra.golani@weizmann.ac.il">ofra.golani@weizmann.ac.il</a><br>
<a href="http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/ab">http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/ab</a><br>
out<br>
-service<br>
<br>
<br>
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