[ome-users] Problem loading Micro-manager files with Bioformats importer

[Sebastien Besson (Staff)]

Hi Kurt,

many thanks for the report and the uploaded sample files. We were able to reproduce the
exception below using Bio-Formats 5.2.2 and I have created a card to track the investigation [1].

The issue comes from the underlying assumption of the MicroManagerReader that the TIFF
files will be named as img_00000000t_channel_00z.tif [2]. However this is not true in this
fileset which is why the dimensions are read incorrectly. We will be in contact with the Micro-Manager
team to clarify what should be expected when reading these filesets.

Best,
Sebastien

[1] https://trello.com/c/n6aaUC9u/47-micromanager-separate-image-files-illegalargumentexception
[2] https://micro-manager.org/wiki/Micro-Manager_File_Formats#Separate_image_files

On 16 Sep 2016, at 19:08, Thorn, Kurt <Kurt.Thorn at ucsf.edu<mailto:Kurt.Thorn at ucsf.edu>> wrote:

Hi All -

We have some Micro-manager files saved as one tiff per channel taken with a recent version of Micro-manager 2.0 that will not open properly in the Bio-formats importer. I've put examples of the problematic files at http://nic.ucsf.edu/MMexamples.zip. I get the following error:

Thanks for your help.
Kurt

java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=1, sizeC=1, sizeT=3, total=27)
at loci.formats.FormatTools.getZCTCoords(FormatTools.java:578)
at loci.formats.in.MicromanagerReader$Position.getFile(MicromanagerReader.java:1125)
at loci.formats.in.MicromanagerReader$Position.getFile(MicromanagerReader.java:1119)
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:444)
at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:298)
at loci.formats.FormatReader.setId(FormatReader.java:1401)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
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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