[ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file

Ofra Golani ofra.golani at weizmann.ac.il
Thu Dec 15 14:05:40 GMT 2016 

HI,

I enabled Java8 and disabled Bio-Formats update site, and repeated the export to ome.tif
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,
However, when the whole export wad done and I tried to open the independent files I had a problem:

-          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”

-          Trying to open one file with Bio-Format Importer I got an exception

loci.formats.FormatException: Unmatched UUID: urn:uuid:28c78877-7c97-4062-a4cc-f5d95b5e403a

                at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:617)

                at loci.formats.FormatReader.setId(FormatReader.java:1399)

                at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)

                at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)

                at loci.plugins.in.Importer.showDialogs(Importer.java:140)

                at loci.plugins.in.Importer.run(Importer.java:76)

                at loci.plugins.LociImporter.run(LociImporter.java:78)

                at ij.IJ.runUserPlugIn(IJ.java:217)

                at ij.IJ.runPlugIn(IJ.java:181)

                at ij.Executer.runCommand(Executer.java:137)

                at ij.Executer.run(Executer.java:66)

                at java.lang.Thread.run(Thread.java:745)

-          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:

-          [cid:image001.png at 01D256C8.CBD46CF0]
The above is the choices I made, and here is the recorded command
run("Bio-Formats Importer", "open=[D:\\UserData\\innaa\\test fiji\\test1\\test1_T17.ome.tif] autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");

Please advise

Ofra


From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Sebastien Besson (Staff)
Sent: Wednesday, December 14, 2016 3:36 PM
To: users OME
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file

HI Ofra,

the issue below also reported in a  screenshot in your previous email matches what was
reported a few days ago [1].
Which update sites do you have enabled? In particular is the Bio-Formats update site [2]
enabled? If so, could you disable it (the Java 8 update site should ship Bio-Formats 5.3.0)
and test whether this solves this export problem?

Best,
Sebastien

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-December/006283.html
[2] http://imagej.net/Bio-Formats#Daily_builds


On 14 Dec 2016, at 12:19, Ofra Golani <ofra.golani at weizmann.ac.il<mailto:ofra.golani at weizmann.ac.il>> wrote:

Hi,

Following on the same problem

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.
I'll upload the file for you to our ftp server, please write me privately and I'll send you the download instructions.
It's a 75 GB file

Note that this time virtual-stack is used, The recorded command is:

run("Bio-Formats Exporter", "save=[D:\\UserData\\innaa\\test<smb://UserData/innaa/test> 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");

The generated ome.tif files cannot be opened with Bio-Formats importer and lead to Exception

(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%)

java.lang.NoClassDefFoundError: ome/xml/meta/MetadataConverter
at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:876)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:554)
at loci.formats.FormatReader.setId(FormatReader.java:1399)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:243)
at ij.io.Opener.open(Opener.java:110)
at ij.io.Opener.openAndAddToRecent(Opener.java:292)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:745)


Best
Ofra




________________________________________
From: ome-users [ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] on behalf of Ofra Golani [ofra.golani at weizmann.ac.il<mailto:ofra.golani at weizmann.ac.il>]
Sent: Wednesday, December 14, 2016 10:10 AM
To: OME User Support List
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file

Hi,

Thanks for looking into this.
I tried to reproduce the problem and it is different from what I wrote before.

In Summary:
1. separating into different ome.tif files for each time points - works OK
2. separating into different tif files for each time points - produce file with corrupted pixel values (only first slice is OK)
3. saving hyperstack into one ome.tif produce file which is missing one image and cannot be rearranged into hyperstack correctly.
4. saving hyperstack into one tif produce file of the correct size but with corrupted pixel values (only first slice is OK)
5. saving hyperstack into one tif with regular Fiji Save As tif works fine

I uploaded sample files for you into my box folder: https://weizmann.box.com/s/xhbixjp0ydbd5qd69s2xnm9k2lugvdri
It also reproduced with the Mitosis sample file

See details below

Best Regards
Ofra


Details:
=====


BioFormats version: 5.3.0-SNAPSHOT,  Build Date: 9 decemebr 2016

Here is my recorded command when saving in tif format
       run("Bio-Formats Exporter", "save=D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito1.tif<smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/Mitosis/mito1.tif> write_each_timepoint compression=Uncompressed");

I opened the file of the first time-point ("mito1_T0.tif")
Attached are snapshots comparing the slices to the original slices and the corrupted file itself

Here is the recorded command for saving in ome.tif format
       run("Bio-Formats Exporter", "save=D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\Mitosis\\mito2.ome.tif<smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/Mitosis/mito2.ome.tif> write_each_timepoint compression=Uncompressed");

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).
When I try to open it with BioFormats Importer I get an exception (attached)

The same behavior reproduced on my workstation (Windows7, which has Release 5.3.0-SNAPSHOT build date 5 December 2016, see attachment)

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.

I crop part of the big file (95 GB) so that I have now 16 slices * 11 time points

- 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:
run("Bio-Formats Exporter", "save=D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP.ome.tif<smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/AllTP.ome.tif> compression=Uncompressed");

- exporting into into one tif file produces hyperstack of the correct size, but with corrupted pixel values

run("Bio-Formats Exporter", "save=D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP.tif<smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/AllTP.tif> compression=Uncompressed");

- 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

saveAs("Tiff", "D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\AllTP_SaveAsTif.tif");


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

run("Bio-Formats Exporter", "save=D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.ome.tif<smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/SepTP.ome.tif> write_each_timepoint compression=Uncompressed");

produce valid stacks - so no problem here

When writing into tif the output files have corrupted pixel values

run("Bio-Formats Exporter", "save=D:\\UserData\\innaa\\OfraTest\\dlGFP_Test_NewFiji\\tmp\\SepTP.tif<smb://UserData/innaa/OfraTest/dlGFP_Test_NewFiji/tmp/SepTP.tif> write_each_timepoint compression=Uncompressed");








-----Original Message-----
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Balaji Ramalingam (Staff)
Sent: Tuesday, December 13, 2016 5:56 PM
To: OME User Support List
Subject: Re: [ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file

Hi Ofra,

Thank you for reporting your issue.
Testing the same locally, we were unfortunately unable to reproduce the bug.

I have recorded the Fiji/ImageJ operations that I had performed (using the Fiji/ImageJ macro recorder) and I have pasted the same here,

run("Bio-Formats Exporter",
"save=/Users/bramalingam/Desktop/FijiExportTest/mitosisOmeTiff/mitosis_time
point_.ome.tif write_each_timepoint compression=Uncompressed²);

I reimported the resultant images back into Fiji/ImageJ and compared the pixel data with the original image.

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, https://imagej.net/Introduction_into_Macro_Programming#The_recorder


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)

You can get the same by selecting,
Help‹>About Plugins‹>Bio-Formats PluginsŠ (in the Fiji menu)

Or by running the following macro command, run("Bio-Formats Plugins...²);

This would help us troubleshoot the issue in better detail.

Best,
Balaji


__________________
Mr Balaji Ramalingam
Software Developer

OME Team
School of Life Sciences
University of Dundee






On 12/12/2016, 14:54, "ome-users on behalf of Ofra Golani"
<ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of ofra.golani at weizmann.ac.il<mailto:ofra.golani at weizmann.ac.il>> wrote:


Hi,

I encounter a problem when using Bio-Formats exporter to save each
time-point into separate file.
It saves into separate files, but the files are corrupted. You see this
when you move through the slices.
You can try this with the "Mitosis" 5D stack of Fiji Sample files.
The problem happens when I save files both as tif and as ome.tif.
I use the latest Fiji version, with the latest Bio-Formats version.

Please advise,
Thanks,

Ofra

----------------------------------------

Ofra Golani

BioImage Analyst
Life Sciences Core Facilities
Weizmann Institute of Science
Tel: +972-8-934-5177
ofra.golani at weizmann.ac.il<mailto:ofra.golani at weizmann.ac.il>
http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/ab
out
-service


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