Having difficulty opening a .lif file in Fiji

Hi there,

I’m trying to open my .lif files in Fiji or ImageJ. A colleague in another department showed me how to do this and it worked fine. He then copied the folder he runs Fiji from into my server and I tried doing the same thing but it doesn’t work. I also tried a work around from this forum (Unable to open .lif files in Fiji on a mac after disrupted update which also hasn’t worked.

Many thanks for your help.

Hi @adam5 and welcome to the forum!

Would you mind trying to open the image with a freshly downloaded Fiji from here:

As Fiji ships with Bio-Formats, opening .lif files should work out of the box…


If that doesn’t help, please copy and paste the entire error message from the Console. In your screenshot, the most important part at the end of the stack trace is missing.

Hi, thanks for the welcome.

That’s actually worked now. I now have my images open. However in the console box I now get this message:

“[INFO] Reading available sites from https://imagej.net/
Reading header
Finding image offsets
[WARN] Unknown Immersion value ‘null’ will be stored as “Other”
[WARN] Unknown Correction value ‘null’ will be stored as “Other”

[WARN] Unknown Immersion value ‘null’ will be stored as “Other”
[WARN] Unknown Correction value ‘null’ will be stored as “Other”
Reading header
Finding image offsets…
[WARN] Unknown Immersion value ‘null’ will be stored as “Other”
[WARN] Unknown Correction value ‘null’ will be stored as “Other””

If anyone wants to help me solve the previous error, the full message was:

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.formats.IFormatReader.getChannelDimLengths()[I
at loci.plugins.in.ImagePlusReader.constructSliceLabel(ImagePlusReader.java:584)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:385)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:230)
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:230)
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:748)

[ERROR] null
java.lang.NoSuchMethodException: Could not find method loci.formats.IFormatReader.getChannelDimLengths()[I
There was a problem with the class loci.formats.IFormatReader which can be found here:
/Z:/AG_Kosan/Adam/Microscopy/Fiji/jars/bio-formats/formats-api-6.2.1.jar
/Z:/AG_Kosan/Adam/Microscopy/Fiji/plugins/Squassh3C_.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.formats.IFormatReader.getChannelDimLengths()[I
at loci.plugins.in.ImagePlusReader.constructSliceLabel(ImagePlusReader.java:584)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:385)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:230)
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:230)
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:748)

at loci.plugins.in.ImagePlusReader.constructSliceLabel(ImagePlusReader.java:584)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:385)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:230)
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:230)
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:748)

Hi @adam5,

I think one of the major issues here is due to the conflict highlighted in these lines

There was a problem with the class loci.formats.IFormatReader which can be found here:
/Z:/AG_Kosan/Adam/Microscopy/Fiji/jars/bio-formats/formats-api-6.2.1.jar
/Z:/AG_Kosan/Adam/Microscopy/Fiji/plugins/Squassh3C_.jar

It looks like the Squassh3C plugin is redistributing a copy of Bio-Formats which conflicts with the one shipped by the Java-8 update site. Are you using an update site for installing the plugin? Is it possible to get in touch with the maintainers and ask them to update the plugin to only ship their own code?

Best,
Sebastien

1 Like