Bug 760 – BioFormats 5.0.2 cannot open some CZI files

Bug 760 - BioFormats 5.0.2 cannot open some CZI files


Summary:	BioFormats 5.0.2 cannot open some CZI files

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Bio-Formats
Version:	unspecified
Hardware:	PC Windows

Importance:	P5 major
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-06-06 03:58 CDT by Sebastian Rhode
Modified:	2014-06-26 07:57 CDT
CC List:	4 users (show)

See Also:

Description Sebastian Rhode 2014-06-06 03:58:55 CDT

Hi,

my Fiji was updated yesterday with all the new ImageJ2 Stuff and it is using BioFormats 5.0.2. Nevertheless it fails to open some CZI file which older version of BioFormats could open (5.0.0 revision cd2a5db works).

New new version does not fail to open this:

https://dl.dropboxusercontent.com/u/623476/Count_Cells_DAPI_10_Frames_with_Fiji.czi

But it does not work for this:

https://dl.dropboxusercontent.com/u/623476/CZI_Problem_Experiment-07-Scene-01-P1-A1.czi


It would really help me, if you guys can tell me difference between those two files causes the problem. Maybe it is something on our side? 


Error Message:

(Fiji Is Just) ImageJ 2.0.0-rc-2-SNAPSHOT; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 32MB of 6127MB (<1%)
 
java.lang.ArrayIndexOutOfBoundsException: 1
	at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2162)
	at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1186)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:691)
	at loci.formats.FormatReader.setId(FormatReader.java:1315)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at ij.IJ.run(IJ.java:271)
	at ij.IJ.run(IJ.java:249)
	at ij.macro.Functions.doRun(Functions.java:593)
	at ij.macro.Functions.doFunction(Functions.java:89)
	at ij.macro.Interpreter.doStatement(Interpreter.java:226)
	at ij.macro.Interpreter.doStatements(Interpreter.java:214)
	at ij.macro.Interpreter.run(Interpreter.java:111)
	at ij.macro.Interpreter.run(Interpreter.java:81)
	at ij.macro.MacroRunner.run(MacroRunner.java:139)
	at java.lang.Thread.run(Thread.java:662)

Comment 1 Melissa Linkert 2014-06-06 05:13:55 CDT

The same issue (with a different file) was reported against Bio-Formats yesterday: https://github.com/openmicroscopy/bioformats/issues/1148

Comment 2 Curtis Rueden 2014-06-23 17:10:49 CDT

It looks like Melissa's fix made it onto the Bio-Formats dev_5_0 branch, meaning it should now be available from the "Bio-Formats" update site.

Can you please try enabling that update site and see if it fixes the issue for you?

Comment 3 Sebastian Rhode 2014-06-24 09:57:27 CDT

Hi Curtis,

I have the Bio-Formats site enabled, but so far it still says BioFormats 5.0.1-DEV under "About Plugins". And the error message is still the same. So The fix is not yet available via the update site.

But I will check back tomorrow.

Cheers, Sebi

Comment 4 Curtis Rueden 2014-06-24 10:41:23 CDT

Hmm, it seems the daily script that updates the Bio-Formats site has been failing silently for a while.

I fixed the problem, and you should get the new version of Bio-Formats if you run the updater again.

Comment 5 Sebastian Rhode 2014-06-25 09:30:52 CDT

Hi Curtis,

now I got 5.0.2 and the problem is gone. The CZI file open as expected, so you can close this entry.

Thanks a lot, Sebi

Comment 6 Johannes Schindelin 2014-06-25 10:14:02 CDT

Sebi, thanks for confirming the fix!

Out of curiosity: do you see those comboboxes under the comment field, prefixed with "Status"? It *should* be possible for users to update the status to "RESOLVED"... if not, that is a bug I'd like to know about ;-)

Comment 7 Sebastian Rhode 2014-06-25 10:51:19 CDT

Hi Johannes,

yes, I see those boxes, but I was afraid to set it to "RESOLVED" by myself (since this is sometimes the rule when working inside a company - only Validation or developers are allowed to set a bug to "Resolved". 
I am happy to hear that it would be fine with guys if I do this by myself next time.

Cheers, Sebi

Comment 8 Johannes Schindelin 2014-06-25 11:58:25 CDT

> I was afraid to set it to "RESOLVED" by myself

Don't be! Fiji is a friendly, collaborative project. There are no hard rules (except the rule of thumb that you should treat people respectfully, at least if you want something from them ;-)).

So feel free to mark this bug as RESOLVED and bask in the glory!