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HI Ofra,
<div class=""><br class="">
</div>
<div class="">the issue below also reported in a screenshot in your previous email matches what was</div>
<div class="">reported a few days ago [1].</div>
<div class="">Which update sites do you have enabled? In particular is the Bio-Formats update site [2]</div>
<div class="">enabled? If so, could you disable it (the Java 8 update site should ship Bio-Formats 5.3.0)</div>
<div class="">and test whether this solves this export problem?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html" class="">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html</a> </div>
<div class="">[2] <a href="http://imagej.net/Bio-Formats#Daily_builds" class="">http://imagej.net/Bio-Formats#Daily_builds</a></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 14 Dec 2016, at 12:19, Ofra Golani <<a href="mailto:ofra.golani@weizmann.ac.il" class="">ofra.golani@weizmann.ac.il</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">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.
<br class="">
It's a 75 GB file<br class="">
<br class="">
Note that this time virtual-stack is used, The recorded command is: <br class="">
<br class="">
run("Bio-Formats Exporter", "save=[D:<a href="smb://UserData//innaa//test" class="">\\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 class="">
<br class="">
The generated ome.tif files cannot be opened with Bio-Formats importer and lead to Exception
<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" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>] on behalf of Ofra Golani [<a href="mailto:ofra.golani@weizmann.ac.il" 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: <a href="https://weizmann.box.com/s/xhbixjp0ydbd5qd69s2xnm9k2lugvdri" 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" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito1.tif</a> 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" 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" 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" 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" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.ome.tif</a> 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" class="">\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.tif</a> 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" 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" 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" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of
<a href="mailto:ofra.golani@weizmann.ac.il" class="">ofra.golani@weizmann.ac.il</a>> wrote:<br class="">
<br class="">
<blockquote type="cite" 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" class="">ofra.golani@weizmann.ac.il</a><br class="">
http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/ab<br class="">
out<br class="">
-service<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
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ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
<br class="">
<br class="">
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