How to open lif file with updated Fiji

After updating Fiji, I can not open my old file of “Lif”. I got the window as below,

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.52n; Java 1.8.0_131 [64-bit]; Mac OS X 10.9.5; 53MB of 2030MB (2%)
 
java.lang.NoClassDefFoundError: loci/common/DebugTools
	at loci.plugins.LociImporter.run(LociImporter.java:69)
	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 net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)
	at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)
	at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)
	at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
	at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)
	at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)
	at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)
	at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)
	at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)
	at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)
	at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)
	at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)
	at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)
	at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Could you provide said file for us to have a look at.

Thank you!

1 Like

How to upload it? I just found this community.

You can zip the file and upload it via the provided file upload:

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@Wuxia the error you pasted above seems to indicate one of the dependencies of Bio-Formats, ome-common, is missing in your Fiji installation. Can you confirm your Fiji is up-to-date and can you tell us about which update sites have been enabled?

1 Like

Thanks for the responses!!

I have uploaded the file in Zip.

Regarding Fiji updating, it is always done automatically after I approves it. I actually do not know how it is got updated and from which specific website. It acts automatically.

I think I uploaded the file twice, but do not know where to check.

When you reply in the forum you will see above the text field the button I pointed out to you.

Please press this and then choose the location of your zipped file on your computer. The file should then appear in your response the same way the screenshot here appeared: How to open lif file with updated Fiji

1 Like

!

Can you see it? This was what happened when I upload the file. I screenshot the process.

There was 3% of uploading, and then it disappeared and a window of “Type here. Use Markdown, BBCode, or HTML to format. Drag or paste images” comes out.

The zip I wanted to upload is 45M. Is it too big?

Hm, I suspect that it is too large. But I did not find any description about that in the Forum docu. @moderators @etadobson is there any info on that?

Would it be possible to provide it by other means. Usually institutions provide means for providing large data for download from collaborators somehow. You would need to get in touch with your IT department for that.

2 Likes

Hi @Wuxia, this is indeed being caused by a missing ome-common dependency in Bio-Formats. In your Fiji installation, there is the folder jars/Bio-Formats, if this is missing ome-common then it will need to be installed.

To install or update the jar please follow the below instructions:

  • In Fiji go to: Help > Update > Manage Update Sites
  • Ensure that the Java 8 site is selected. Then go back back and into Advanced Mode
  • From here search for ome-common with the View Option as View all files
  • This should find ome-common-6.0.3.jar which you can select and install
3 Likes

“Maximum number of megapixels allowed for an image = 40” is the closest I can find. ~J

2 Likes

Following the instruction, I updated Fiji and could finally open the file. Thank your guys very very much!!

1 Like

A post was split to a new topic: Another problem when loading the .lif or .czi files by using Bio-Formats Importer