[ome-users] Abberior MSR files - having trouble opening them with Fiji and ImageJ

[David Gault (Staff)]

Hi Jacqueline,

Thank you for submitting the QA files. I was able to reproduce the issue as you described. From debugging the problem it appears that some of the embedded XML metadata within the file is not valid. We will contact the developers responsible for the format to try and resolve the issue. I have opened a Trello card on the Bio-Formats inbox to track the issue https://trello.com/c/GHhVlBxM/229-obfreader-invalid-ome-xml.

Can you confirm if the sample files provided can be published under a CC-BY license (http://downloads.openmicroscopy.org/images/)?

With Thanks,
David Gault

On 7 Mar 2018, at 23:43, Jacqueline Ross <jacqui.ross at AUCKLAND.AC.NZ<mailto:jacqui.ross at AUCKLAND.AC.NZ>> wrote:

Hi everyone,

Further to my previous email, I have now uploaded 2 x datasets. The one that I can open is called #12.msr. The one I can’t open is called Brain_01.msr

Kind regards,

Jacqui

From: Jacqueline Ross
Sent: Thursday, 8 March 2018 12:29 p.m.
To: 'ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>' <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Abberior MSR files - having trouble opening them with Fiji and ImageJ

Hi everyone,

I'm having trouble opening some MSR files acquired on an Abberior STED system. Some are opening but others aren't and I get the error shown below in those cases. I updated my Fiji version and also tried putting the latest version of Bioformats in ImageJ to no avail. Some of these will be z stacks but not all.

Interestingly, it is all of the files we acquired later that we can’t open. The first ones were fine. I’m not sure if the first one we can’t open is a z-stack and if that somehow has caused a problem with the rest. We don’t have the Abberior system here so don’t have the original software available to open the files. I will upload some files but can’t provide metadata or screenshots for the problem files as I can’t open them with Fiji and don’t have the original data. I will upload one file that I can open together with its metadata.

I am running the latest Fiji version  (ImageJ 1.51u) with Bio-Formats Release 5.8.1 – see attached screenshots. I also couldn’t open these files with an older compilation or on our Mac so I don’t think it’s platform-specific. I am using a 64bit Windows computer with Java 1.8.

Can anyone help? It would be very much appreciated.

(Fiji Is Just) ImageJ 2.0.0-rc-65/1.51u; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 66MB of 100000MB (<1%)
java.lang.IllegalArgumentException: 0 must not be null and positive.
               at ome.xml.model.primitives.PositiveInteger.<init>(
PositiveInteger.java:48)
               at loci.formats.MetadataTools.populatePixelsOnly(
MetadataTools.java:288)
               at loci.formats.MetadataTools.populateMetadata(
MetadataTools.java:251)
               at loci.formats.MetadataTools.
populatePixels(MetadataTools.java:151)
               at loci.formats.MetadataTools.
populatePixels(MetadataTools.java:97)
               at loci.formats.in.OBFReader.initFile(OBFReader.java:217)
               at loci.formats.FormatReader.setId(FormatReader.java:1397)
               at loci.plugins.in.ImportProcess.
initializeFile(ImportProcess.java:499)
               at loci.plugins.in.ImportProcess.
execute(ImportProcess.java:142)
               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:221)
               at ij.IJ.runPlugIn(IJ.java:185)
               at ij.IJ.runPlugIn(IJ.java:174)
               at HandleExtraFileTypes.openImage(
HandleExtraFileTypes.java:499)
               at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
               at ij.IJ.runUserPlugIn(IJ.java:221)
               at ij.IJ.runPlugIn(IJ.java:185)
               at ij.IJ.runPlugIn(IJ.java:174)
               at ij.io.Opener.openWithHandleExtraFileTypes(
Opener.java:515)
               at ij.io.Opener.openImage(Opener.java:369)
               at ij.io.Opener.openImage(Opener.java:242)
               at ij.io.Opener.open(Opener.java:109)
               at ij.io.Opener.openAndAddToRecent(Opener.java:291)
               at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
               at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
               at java.lang.Thread.run(Thread.java:745)

Kind regards,

Jacqui


Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit (BIRU)
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Telephone: Ext 87438; DDI:  +64 9 923 7438

Website:    http://www.auckland.ac.nz/biru



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