SlideBook sld files not opening after last update (july2018)

fiji
bio-formats
imagej
native-lib-loader

#1

Hi,

I have always been able to open the SlideBook (.sld) files from the 3i directly into Fiji. Unfortunately, since the last usual updating (July2018), when I try to open them, I can not; this is the message it appears:

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 64MB of 5000MB (1%)
 
java.lang.NullPointerException at org.scijava.nativelib.NativeLibraryUtil.getPlatformLibraryPath(NativeLibraryUtil.java:189)
	at org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(NativeLibraryUtil.java:308)
	at loci.formats.services.JPEGTurboServiceImpl.<init>(JPEGTurboServiceImpl.java:107)
	at loci.formats.in.NDPIReader.<init>(NDPIReader.java:69)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
	at java.lang.Class.newInstance(Class.java:442)
	at loci.formats.ImageReader.<init>(ImageReader.java:129)
	at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:77)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
	at java.lang.Class.newInstance(Class.java:442)
	at loci.formats.ImageReader.<init>(ImageReader.java:129)
	at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:619)
	at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
	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:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.IJ.runPlugIn(IJ.java:181)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
	at ij.io.Opener.openImage(Opener.java:369)
	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 shall say that I have always ticked for udating the Bio-Formats and the Java8 sites. This is the first time I have issues, so is it possible this is a bug?

Any help would be much appreciate it.

Cheers


#2

Hi,

I have a very similar issue (almost identical error message) with Olympus image files (OIB) since today. Never happened before. (The last Life-Line version works fine https://imagej.net/Fiji/Downloads).

Any support would be very much appreciated.

Thanks.


#3

Please see my answer on this related forum topic:


#4

It worked! (I had to stop ImageJ process on the Task Manager before because even with Fiji closed it wouldn’t allow me to delete the native-lib-loader-2.3.0.jar, but I finally could)

Thank you so much! Much appreciated!


#5

I had a similar problem with bio-formats opening slide book; I followed the suggestion above, and this allowed bio-format importer to open (an improvement), but it stalled there eventually giving me the following “exceptions”. I feel like this started with the latest version of Java 8, but I could be wrong.

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit]; Mac OS X 10.13.5; 890MB of 10667MB (8%)
 
java.lang.ArrayIndexOutOfBoundsException: 0
	at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
	at loci.formats.FormatReader.setId(FormatReader.java:1397)
	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:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.IJ.runPlugIn(IJ.java:181)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
	at ij.io.Opener.openImage(Opener.java:369)
	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)

#6

Hi @Ken,

have you tried enabling the native Bio-Formats Slidebook reader developed and maintained by Intelligent Imaging for opening your files? See https://www.intelligent-imaging.com/technical-answers#SLDinFIJI for more details.

Best,
Sebastien


#7

@s.besson Yes, the slidebook reader is selected in the plugin manager settings. To be clear, this was all working smoothly until a recent update in Fiji/Image J and Java 8 171, build 11.


#8

Thanks,

the 3i Slidebook reader makes use of the native-lib-loader library which was upgraded in the recent Fiji update causing the issue reported in this thread. I assume you applied the workaround suggested by @imagejan in SlideBook sld files not opening after last update (july2018).
Which update site do you have enabled and can you confirm jars/native-lib-loader-2.2.0.jar is installed in your Fiji distribution? We will try and reproduce locally.

Best,
Sebastien


#9

Thanks Sebastien. Yes, I read the previous suggestion and I did change to 2.2.0. This improved things as the BioFormat window now opens - it didn’t with the newer version of native-lib-loader. However, Image J does not progress. It takes up a lot of CPU time, and eventually gives me the exceptions I posted above.


#10

Hi @Ken,

I tested with the following local distribution:

  • OS X 10.13.5
  • (Fiji Is Just) ImageJ 2.0.0-rc-28/1.52d; Java 1.8.0_66 [64-bit]
  • ImageJ, Fiji, Java-8 and Slidebook update sites enabled

With these, I was able to successfully open a recent Slidebook file that cannot be opened using the legacy Slidebook reader. Disabling the Slidebook update site, uninstalling the 3i slidebook Jar and restarting Fiji leads to an exception while opening the file.

One navie idea, have you re-run a Fiji update in the last few days? I know @ctrueden pushed to the Java-8 update site to revert some of the recent changes for investigation (see https://list.nih.gov/cgi-bin/wa.exe?A2=ind1807&L=IMAGEJ&F=&S=&P=33276) so doing so should be harmless.

Best,
Sebastien