Abberior MSR files - having trouble opening them with Fiji and ImageJ
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Abberior MSR files - having trouble opening them with Fiji and ImageJ
 
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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. I saw that someone had trouble previously with these file types but the problem had apparently been sorted out. I'm thinking it's something to do with my Java version...? 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Jacqui,
That looks like a bug in Bio-Formats. I'd suggest reporting it to the OME team as described here: http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Mon, Mar 5, 2018 at 5:42 PM, Jacqueline Ross <[hidden email]> wrote: > 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. I saw that someone had trouble > previously with these file types but the problem had apparently been sorted > out. I'm thinking it's something to do with my Java version...? > > 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 > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ
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Hi Curtis,
Thanks for your reply. I'll do that. I wondered if it was something to do with the pyramid structure but the first data set is also pyramid (multiple images) and it's OK. Kind regards, Jacqui -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Wednesday, 7 March 2018 10:10 a.m. To: [hidden email] Subject: Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ Hi Jacqui, That looks like a bug in Bio-Formats. I'd suggest reporting it to the OME team as described here: http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Mon, Mar 5, 2018 at 5:42 PM, Jacqueline Ross <[hidden email]> wrote: > 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. I saw that > someone had trouble previously with these file types but the problem > had apparently been sorted out. I'm thinking it's something to do with my Java version...? > > 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 > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ
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Hi Jacqui,
Improvements have been made to this reader in Bio-Formats 5.8.0 [1]. If you can confirm you are using this version of Bio-Formats, this error could be a side-effect. From the OME side, we will minimally need sample files reproducing the issue as explained in the link sent by Curtis. Note that as the reader is also maintained by people outside the OME team, sharing samples that could be published under a CC-BY license [2] would be strongly recommended so that we can discuss the resolution of the issue with them. Best, Sebastien [1] http://docs.openmicroscopy.org/bio-formats/5.8.0/about/whats-new.html [2] http://downloads.openmicroscopy.org/images/ On 7 Mar 2018, at 05:33, Jacqueline Ross <[hidden email]<mailto:[hidden email]>> wrote: Hi Curtis, Thanks for your reply. I'll do that. I wondered if it was something to do with the pyramid structure but the first data set is also pyramid (multiple images) and it's OK. Kind regards, Jacqui -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Wednesday, 7 March 2018 10:10 a.m. To: [hidden email]<mailto:[hidden email]> Subject: Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ Hi Jacqui, That looks like a bug in Bio-Formats. I'd suggest reporting it to the OME team as described here: http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Mon, Mar 5, 2018 at 5:42 PM, Jacqueline Ross <[hidden email]> wrote: 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. I saw that someone had trouble previously with these file types but the problem had apparently been sorted out. I'm thinking it's something to do with my Java version...? 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html The University of Dundee is a registered Scottish Charity, No: SC015096 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ
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Hi Sebastien,
Thanks for your reply. Yes, I am using Bio-Formats 5.8.0 as I upgraded to the latest version when I experienced the problem. I saw it with the previous version as well. There's no problem with sharing a couple of data sets as they are test images. Kind regards, Jacqui -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Sebastien Besson (Staff) Sent: Wednesday, 7 March 2018 7:58 p.m. To: [hidden email] Subject: Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ Hi Jacqui, Improvements have been made to this reader in Bio-Formats 5.8.0 [1]. If you can confirm you are using this version of Bio-Formats, this error could be a side-effect. From the OME side, we will minimally need sample files reproducing the issue as explained in the link sent by Curtis. Note that as the reader is also maintained by people outside the OME team, sharing samples that could be published under a CC-BY license [2] would be strongly recommended so that we can discuss the resolution of the issue with them. Best, Sebastien [1] http://docs.openmicroscopy.org/bio-formats/5.8.0/about/whats-new.html [2] http://downloads.openmicroscopy.org/images/ On 7 Mar 2018, at 05:33, Jacqueline Ross <[hidden email]<mailto:[hidden email]>> wrote: Hi Curtis, Thanks for your reply. I'll do that. I wondered if it was something to do with the pyramid structure but the first data set is also pyramid (multiple images) and it's OK. Kind regards, Jacqui -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Wednesday, 7 March 2018 10:10 a.m. To: [hidden email]<mailto:[hidden email]> Subject: Re: Abberior MSR files - having trouble opening them with Fiji and ImageJ Hi Jacqui, That looks like a bug in Bio-Formats. I'd suggest reporting it to the OME team as described here: http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Mon, Mar 5, 2018 at 5:42 PM, Jacqueline Ross <[hidden email]> wrote: 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. I saw that someone had trouble previously with these file types but the problem had apparently been sorted out. I'm thinking it's something to do with my Java version...? 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html The University of Dundee is a registered Scottish Charity, No: SC015096 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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