Fiji does not open DeltaVision .dv files with Bioformat Importer window anymore

fiji
bio-formats
imagej
native-lib-loader

#1

Hi,

Fiji suddenly stopped opening .dv files with Bio-Format Importer anymore, it doesn’t open the files at all and gives me this message:

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 30MB of 2978MB (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:423)
	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:423)
	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.open(Opener.java:72)
	at ij.plugin.Commands.run(Commands.java:27)
	at ij.IJ.runPlugIn(IJ.java:198)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)

I tried re-installing Fiji multiple times and updating Bio-Formats plugins nothing worked :frowning:

Thank you very much in advance.


#2

I can reproduce this problem with an up-to-date Fiji installation. The issue is caused by the library native-lib-loader-2.3.0.jar in the ./Fiji.app/jars folder.

As a workaround, you can downgrade to version 2.2.0 of this file by deleting it and replacing it with native-lib-loader-2.2.0.jar downloaded from here:

http://maven.imagej.net/service/local/repositories/central/content/org/scijava/native-lib-loader/2.2.0/native-lib-loader-2.2.0.jar

This worked for me for opening czi files which are also opened via the Bio-Formats importer.

UPDATE:

Thanks to @ctrueden, the Java-8 update site now ships native-lib-loader-2.2.0.jar again for the time being, until the issues with the newer version are resolved. So if you still encounter this issue, just run the updater again.


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#3

It worked!!! It really worked! I am literally about to cry :grinning: from happiness. Thank you so much!