[ome-users] Micro-Manager datasets can't be opened anymore

[Sebastien Besson (Staff)]

Hi Thomas,

I think you are encountering the issue reported in [1].

The formats-common component has been decoupled, renamed as ome-common and
supplemented with new methods in Bio-Formats 5.3.0. However, the old formats-common
JAR is still shipped via the Fiji update site and seems to conflict with the newer JAR shipped
via the Java-8 update site.

A workaround is to uninstall formats-common.jar locally [2]. There is still some discussion
on the preferable way to resolve this generically which probably involve work on the various
update sites.

Best,
Sebastien

[1] http://forum.imagej.net/t/fiji-and-bioformats-conflicting-jars/5736
[2] http://forum.imagej.net/t/fiji-and-bioformats-conflicting-jars/5736/3


> On 9 Jul 2017, at 11:33, Thomas Julou <thomas.julou at normalesup.org> wrote:
>
> Hello,
>
> For 1 or 2 months, I can’t open Micro-Manager datasets anymore. More specifically, I try to open datasets stored using stack formats, with the Import>Bio-Formats menu of Fiji (IJ 1.51n, BF 5.5.3 built 5 July 2017).
>
> The error reported is pasted below.
> Thank you in advance for letting me know if you can reproduce it on demo datasets.
>
> Best,
> Thomas
>
> --
> Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 207 16 21
>
>
>> WARNING: multiple locations found!
>> java.lang.NoSuchMethodError: loci.common.RandomAccessInputStream.readUnsignedInt()J
>> at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1237)
>> at loci.formats.tiff.TiffParser.getFirstOffset(TiffParser.java:365)
>> at loci.formats.tiff.TiffParser.getFirstIFD(TiffParser.java:319)
>> at loci.formats.in.SEQReader.isThisType(SEQReader.java:73)
>> at loci.formats.FormatReader.isThisType(FormatReader.java:615)
>> at loci.formats.ImageReader.getReader(ImageReader.java:185)
>> at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:618)
>> at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
>> 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.Executer.runCommand(Executer.java:137)
>> at ij.Executer.run(Executer.java:66)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1237)
>> at loci.formats.tiff.TiffParser.getFirstOffset(TiffParser.java:365)
>> at loci.formats.tiff.TiffParser.getFirstIFD(TiffParser.java:319)
>> at loci.formats.in.SEQReader.isThisType(SEQReader.java:73)
>> at loci.formats.FormatReader.isThisType(FormatReader.java:615)
>> at loci.formats.ImageReader.getReader(ImageReader.java:185)
>> at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:618)
>> at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
>> 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.Executer.runCommand(Executer.java:137)
>> at ij.Executer.run(Executer.java:66)
>> at java.lang.Thread.run(Thread.java:745)
>
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