CZI files from ZEN Blue cause errors

On a recent CZI file saved with Zen Blue, we encounter a problem when reading certain files.
I’ve attached the culprit files here in case a kind BioFormats soul can have alook and give me a hand…

Thanks for any insight

Oli

(Fiji Is Just) ImageJ 2.0.0-rc-71/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 1124MB of 48998MB (2%)
 
java.lang.NumberFormatException: For input string: "2,2"
	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)

From what version of Zen Blue and which system are those files?

I use BioFormats dauly to open CZI files and did not encounter problems so far.

Sebi (from Zeiss)

We got these images from an lsm900 airyscan. Something in the metadata isn’t parsed properly… Have you managed to open the files?

Best

Oli

It seems the detector zoom metadata is listed as 2,2 which is throwing the exception when parsed to a Double. This may be down to the system locale and modifying this one value allows the files to open as expected. The first file on the drive however still fails as its not been able to locate any planes.

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Dear @dgault

Thanks for the info! Are you saying I should change the locale of the system trying to open the file or of the system that saved the file?

In the medium to long term Bio-Formats may be able to better handle formatting to different locales. In the short term, using a different locale on the system writing the files may resolve the issue for you (any that use ‘.’ as the decimal separator).

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In Zen Blue i always go to Tools & Options for that reason and set the decimal separator to “., switch off the thousand separator and set language in Zen manually to English.

Let me know if you could resolve the issue.

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I seem to have a similar issue (reported here Opening LSM 980 (Airyscan 2) .czi files using Bioformats ... error).

So if I understand this correctly I need to change the locale on the acquisition computer such that it uses . as the decimal separator and then the acquired images in Fiji.

Does Bioformats use the system local for opening those files? (I.e. can the already written files be opened in Fiji if I set the locale to German or will I manually have to change the decimal seperator in a binary editor ?).

Just wanted to confirm that modifying the 3,3 to 3.3 (multiple occurances) in the .czi file indeed fixes the issue.

@sebi06 : I would argue that for reasons portability and reproducablilty metadata should be encoded in a locale-independent way (unless the locale and encoding is part of the metadata), maybe this would be an enhancement for Zen?

I do not think you need to change the location of the computer. Setting the options in Zen should do the job.

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