Cant open .ics files with Bioformats (in FIJI)

HI all,

I have most probably a really trivial problem. For some reason I cant no longer open .ics files with Bioformats (using FIJI). I get the following exception when using drag and drop:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_66 [64-bit]; Mac OS X 10.14.3; 179MB of 5945MB (3%)
 
java.lang.NoSuchFieldError: canSeparateSeries
	at loci.formats.in.SVSReader.<init>(SVSReader.java:102)
	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:229)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:182)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:229)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:182)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:516)
	at ij.io.Opener.openImage(Opener.java:370)
	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)

Any ideas?

Cheers,
Teemu Ihalainen

Hi @teemui Welcome to image.sc!

Could you tell us which version of the Bio-Formats plugins you are currently using?

Help > About Plugins > Bio-Formats Plugins 

Did you recently update any plugins? It sounds like there’s a mismatch in your libraries somewhere. This happens every so often:

Mostly meaning it should be possible to get you patched up.

Cheers,
~Josh

Sorry, I forgot to mention that:

Bio-Formats Plugins for ImageJ
Release: 6.0.1
Build date: 13 March 2019

Cheers,
Teemu

Thanks @teemui. Can you also give us a list of the update sites that are enabled in your Fiji distribution?

OK, here it comes (the names):

ImageJ
Fiji
Java-8
3D ImageJ Suite
BIG-EPFL
Bio-Formats
Biomedgroup
BioVoxxel
ClearVolume
IJPB-plugins
ImageScience
ImagingFCS
LimeSeg
Morphology
MPIBPC
NucleusJ
Tango
TensorFlow
TIssue Analyzer
Virtual Cell
Deforming Mesh

MPIBPC matches the issue that had been discussed in this thread already mentioned above in Cant open .ics files with Bioformats (in FIJI).

This update site is still ship an outdated and partial version of Bio-Formats which breaks usage of the latest version of the library. Can you try disabling it and trying again?

This topic was automatically closed after 5 days. New replies are no longer allowed.