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

[Jacqueline Ross]

Hi everyone,



I'm having trouble opening some MSR files acquired on an Abberior STED system last week. 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 in the session 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 have uploaded 1 example problem file but can't provide metadata or screenshots. I have also uploaded another file that I can open.



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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