Error opening CZI files with Image J (already installed Bio-Formats plugin)

Hello,

I’ve been trying to open CZI files with Image J. I’ve tried to
import them with the Import function of the Bio-formats plugin but I
get an error message (as you can see in the print screen attached to
this post). Does anyone have any suggestion, please?

Is it a problem with the files? The import options?

I would be most grateful!

Many thanks!

Ines

Welcome to the forum, @InesB!

For some reason, your screenshot doesn’t get displayed. Could you try again, or - even better because it’ll be searchable - paste the plain text of the error message here?

Bio-Formats can open only some types of CZI images, but fails with others, e.g. when you saved with compression enabled on some systems.

Hi,

The error message is the following:

loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
    at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2975)
    at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2947)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:583)
    at loci.formats.FormatReader.setId(FormatReader.java:1426)
    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)

Thanks!!

That’s what it is, the JPEG-XR compression is not (yet) supported by Bio-Formats. Try re-saving the czi files from within the ZEN software without compression.

The good news is: thanks to a partnership with Zeiss, it will be! (Previously, JPEG-XR was not in the cards, but now it is.)

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