⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 423 - stitched czi files still not recognized
stitched czi files still not recognized
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P2 normal
Assigned To: Melissa Linkert
Depends on:
Blocks:
 
Reported: 2012-04-30 14:20 CDT by Silke White
Modified: 2012-06-08 04:11 CDT
0 users

See Also:
Description Silke White 2012-04-30 14:20:31 CDT 
Hi Melissa,

sorry for the new bug report, but the czi - file format story continues: we now have stitched czi files (stitched directly after acquisition in ZEN blue), that don't open in Fiji (see error below). The original unstitched czi data open fine.
I've uploaded "20120425_10x_stiched.czi" into the Fiji uploader as an example file.

Thanks for your help,
Silke

java.lang.ArithmeticException: / by zero
	at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:235)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:123)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:98)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:369)
	at loci.formats.FormatReader.setId(FormatReader.java:1091)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:139)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:79)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	at ij.IJ.runPlugIn(IJ.java:140)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	at ij.IJ.runPlugIn(IJ.java:140)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
	at ij.io.Opener.openImage(Opener.java:288)
	at ij.io.Opener.openImage(Opener.java:309)
	at ij.io.Opener.open(Opener.java:138)
	at ij.io.Opener.openAndAddToRecent(Opener.java:224)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:680)
Comment 1 Melissa Linkert 2012-05-18 16:34:10 CDT 
Thank you for reporting this problem.  The issue is entirely to do with the fact that the images are already stitched, as we have not encountered that particular type of .czi data before.

I am away from now until Monday evening, but will hopefully have a fix shortly after returning.
Comment 2 Melissa Linkert 2012-06-08 04:11:03 CDT 
This is now finally fixed with this commit:

https://github.com/melissalinkert/bioformats/commit/11baca690f163ddd32201fa5b1a070e8a96f0f97

A new build of Bio-Formats containing the fix is not yet available, but the upcoming 4.4.0 release will contain the fix.