Unable to open .lif files in Fiji on a mac after disrupted update

fiji
bio-formats
native-lib-loader
Tags: #<Tag:0x00007fa30f8f0228> #<Tag:0x00007fa30f8f00e8> #<Tag:0x00007fa30f8f7f78>

#1

Dear all,

Earlier today everything was fine and I was working in Fiji on .lif files. Unfortunately there seems to have been a temporary problem with the WiFi while Fiji was downloading an update. I noticed when trying to cut a part of an image out, because the newly generated image was completely black. I quit Fiji and tried to reopen it, but it no longer opened. Concluding that the aborted update must have corrupted the program, I deleted the version of Fiji I had and downloaded another one. This new version (ImageJ 1.52d, Java 1.8.0_172 [64-bit]) does manage to open the program, but fails to open my image files. Whichever way I try, whether via drag&drop, File>Open or File>Import>Bio-Formats, I always get error messages. Using the latter, the error message is:

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_172 [64-bit]; Mac OS X 10.13.5; 139MB of 2464MB (5%)
 
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.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)

I would be very grateful for any tips on how to resolve this issue.
In case this matters, I am using a MacBook Air (13-inch, Mid 2012) running High Sierra (10.13.5).
Thank you!


#2

I could reproduce this problem opening .lsm; .lif or .oir when I used Bio-Formats Importer.

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52d; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 70MB of 24448MB (<1%)

java.lang.NullPointerException


#3

Please see my answer on this related forum topic:


#4

I do have the exact same problem of opening .lif and .czi files. I tried the solution you provide, but I get another message:
The Java JAR file “native-lib-loader-2.2.0.jar” could not be launched. Check the Console for possible error message.

I use a Macbook Pro with High Sierra

Please help!


#5

This solution has worked for me, thank you very much!