Czi files (nullpointerexception)

Hi All,
I attempted to use FIJI to open a .czi file I generated recently. each file contains multiple images, each consisting of multiple tiled z-stacks.

This was the error I got

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51p; Java 1.8.0_121 [64-bit]; Mac OS X 10.12.6; 42MB of 4668MB (<1%)
 
java.lang.NullPointerException
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:698)
	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.IJ.runPlugIn(IJ.java:170)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.IJ.runPlugIn(IJ.java:170)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:514)
	at ij.io.Opener.openImage(Opener.java:368)
	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:745)

I am using a freshly updated vanilla version of FIJI

Dear @W_Masselink,

Could you please check if you have enabled the Java-8 update site? It seems that your Fiji version is still not “up-to-date”. It would be even easier to check if the issue persists when you download and use a completely fresh version of Fiji.

Best,
Stefan

It is a brand new institute provided laptop, but used a managed software centre which restricts installation and downloads of other sources. After getting an admin account set-up I managed to download a fresh copy of fiji (fiji-macosx.dmg) and sort everything out.

There are still some minor issues, such as the console which shows

[WARN] Unkown IlluminationType value 'Fluorescence' will be stored as "Other"

and the files are all separated, not tiled and merged like I saved them originally. I can sort that out though. At least I can open the files now.

Thanks,
Wouter

You can check Plugins > Bio-Formats > Bio-Formats Plugins Configurations and look for Zeiss CZI in the sidebar. There is an Autostitch option that might be what you are looking for.

Those you can safely ignore if you don’t require that meta data.