[ome-users] Fiji error!

Burki, Mubarik z.burki.12 at ucl.ac.uk
Wed Aug 24 10:16:00 BST 2016

Dear David,

I have the 5.2.0 version for Bio-Formats.

I will upload a sample now.

Best wishes,


From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of David Gault (Staff) <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:
OMERO.qa - Open Microscopy Environment<https://www.openmicroscopy.org/qa2/qa/upload/>
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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