Opening LSM 980 (Airyscan 2) .czi files using Bioformats ... error

Hi Bioformats team and @sebi06,

we just got an LSM 980 (Airyscan 2) and it didn’t take long for the first users to come to me and point out that they can’t open their .czi files with Fiji.
I have attached a sample file
ClsPlus_06.zip (3.5 MB)

When trying to open this using the Bioformats importer (freshly updated Fiji - as of today) I get a NumberFormatException.

So I’m not sure whether Zeiss added some new “features” to the the .czi format with the release of the 980 that haven’t made it into Bioformats yet or whether this is an unrelated issue.

For now, I will tell users to also export their images as .tif from ZEN as a workaround if they want to open them with Bioformats, but maybe this is something that can be fixed?

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 84MB of 12101MB (<1%)
 
java.lang.NumberFormatException: For input string: "3,3"
	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
	at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
	at java.lang.Double.parseDouble(Double.java:538)
	at java.lang.Double.<init>(Double.java:608)
	at loci.formats.in.ZeissCZIReader.translateInformation(ZeissCZIReader.java:2364)
	at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1999)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:1128)
	at loci.formats.FormatReader.setId(FormatReader.java:1389)
	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:230)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:182)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:230)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:182)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:516)
	at ij.io.Opener.openImage(Opener.java:370)
	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:748)
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As we might be getting a 900 soon, I would be curious whether this problem affects that system as well!

Any chance it’s the same problem as was reported here: CZI files from ZEN Blue cause errors ?
If so, see the work-around in that message sequence.

Damir

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That looks as if it may be the same problem. I will give it a try.

it is indeed the same issue, will continue discussion in the thread linked to by @dsudar.

I would first set the Zen decimal settings to what you need.

If thar does not help openthe files in Zen Blue and expprt them as OME-TIFF.

Obviously it would be nice if BioFormats can deal with different speparators.

Officially the CZI did not change but the devil is in the details. If the issue remains, let me know and I can try to have a look when I am back in the office in 2 weeks.

2 Likes