Unable to open LIF files on FIJI/Image J

Usage & Issues
#1

Hi,

I am having difficulty opening images with FIJI. The issues started following updates to the software about a month ago.

Here are the current issues:
-I cannot open Leica image files (.lif) by clicking on the file in Finder. I must open the file through FIJI itself.
-Upon opening the file in FIJI, the following pop-up opens

1434Ă—282 24.2 KB

Recently, I tried to open a different file and the following opened instead:
<img src="//discourse-cloud-file-uploads.s3.dualstack.us-west-2.amazonaws.com/business4/uploads/imagej/original/2X/9/9d714b6674072837fb08955b0b323bc067e15bc7.png" width="690"height=“197”>

With the first pop-up, most of the time, the file opens successfully, with the exception of one file, in which the message read:

994Ă—1382 65.2 KB

With the second message, one of the files I was trying to open appeared to be “corrupted”(?) as the following message appeared:

1306Ă—1388 75.2 KB

986Ă—398 22.9 KB

I would love to have any information as to why FIJI is having difficulty opening some of my files. I am basically computer illiterate so any advice would be greatly appreciated.

Thanks in advance.

#2

Hi,

When using Bio-Formats to import images in FIJI the file stitching dialogs you see will be shown if you have selected the option “Group files with similar names” in the Import Options window.

The errors you are seeing are likely because it is attempting to group together files which either do not exist or do not belong together.

If you do not wish to group files then unchecking this option should allow the files to open normally.

David Gault

1 Like
#3

Hi @jmalin319

Welcome to the Forum!

So… can we get a bit more information from you?

  1. What version of ImageJ/Fiji/Java are you running? To find that information… You can click on the status bar to see the versions and report back.
  2. How exactly are you opening your images in ImageJ/Fiji? There are multiple ways to open images actually… but we recommend opening images via File > Import > Bio-Formats - that way your metadata is read in correctly - that goes for .tif and .lif files - most image formats really. You can read up more on Bio-Formats here. Note: there were recent updates to Bio-Formats, so it’s always a good idea to consistently update Fiji, via the Updater, to stay as up-to-date as possible regarding all the plugins, etc. The newest version - 5.5.2 - was just released (see this forum post). If there is still a problem opening your images via Bio-Formats, you can always post a bug report on the Bio-Formats page.

I hope this helps at least get you started in fixing this issue.

eta :slight_smile:

#4

Thanks so much for responding. Unclicking “group files with similar names” allowed me to open all of my files.

re: @etadobson’s questions, I am running (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n and Java 1.8.0_66 [64bit]. I was trying to open images through either clicking on the files in Finder or through File>Open. I am currently unable to open files through clicking in Finder, if anyone has input on that.

#5

Hello,

I know this is an old topic, but I really need some help. I am a very recent user of ImageJ and I will use it to open files from a Leica microscope, my problem is that I am not able to import it with the Bio-Formats plugin, the following errors are shown:

loci.formats.FormatException: C:\Users\YMEDINAG\Documents\FLIM\Test-FLIM-2019-10-07.lif is not a valid Leica LIF file
at loci.formats.in.LIFReader.initFile(LIFReader.java:492)
at loci.formats.FormatReader.setId(FormatReader.java:1389)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
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:230)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.Executer.runCommand(Executer.java:148)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)

Can anyone help me please ? I tried to pen it by using the importer of Bio-Formats and checking and unchecking all the options.

Deep thanks !!!