[ome-users] Fiji error!

[David Gault (Staff)]

Hi Mubarik,

Thank you for uploading the sample file for testing. I was able to reproduce the same error that you encountered.

This is caused by a bug in the Dimension Swap Dialog for the Bio-Formats plugin.
When an image has different dimensions for each series then the dimension swapping dialog was incorrectly displaying and expecting the dimension sizes for the last series in the image.

I have opened a Bio-Formats PR with a proposed fix for this issue:
https://github.com/openmicroscopy/bioformats/pull/2546

With Thanks,
David Gault


On 24 Aug 2016, at 10:16, Burki, Mubarik <z.burki.12 at ucl.ac.uk<mailto:z.burki.12 at ucl.ac.uk>> wrote:

Dear David,

I have the 5.2.0 version for Bio-Formats.

I will upload a sample now.

Best wishes,

Mubarik


________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>>
Sent: 24 August 2016 10:06
To: OME User Support List
Subject: Re: [ome-users] Fiji error!

Hi Mubarik,

Could you tell us which version of Bio-Formats you are currently using?
You can find out by going to Help -> About Plugins -> Bio-Formats Plugins, the version will be listed beside ‘Release’.

Also if it is possible would you be able to upload a sample file for testing to:
https://www.openmicroscopy.org/qa2/qa/upload/
OMERO.qa - Open Microscopy Environment<https://www.openmicroscopy.org/qa2/qa/upload/>
www.openmicroscopy.org<http://www.openmicroscopy.org/>
Uploading sample images. OMERO uses Bio-Formats to help with importing files. Any files listed as a supported format should import into OMERO.



With Thanks,
David Gault


On 23 Aug 2016, at 14:42, Burki, Mubarik <z.burki.12 at ucl.ac.uk<mailto:z.burki.12 at ucl.ac.uk>> wrote:

Dear All,

I am trying to open some files using Fiji that I have previously opened several times. However, I am now unable to open my lif files and  the following error comes up:


 (Fiji Is Just) ImageJ 2.0.0-rc-49/1.51f; Java 1.8.0_66 [64-bit]; Mac OS X 10.9.5; 37MB of 1682MB (2%)

java.lang.IllegalArgumentException: order is unexpected length (4)
at loci.formats.DimensionSwapper.swapDimensions(DimensionSwapper.java:91)
at loci.plugins.in.ImportProcess.initializeDimOrder(ImportProcess.java:575)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:155)
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)

I have tried updating FIJI and reinstalling it. Nothing seems to work.

Please help!
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