LIF cannot open with BioFormats 6.3.0

Hi @OMETeam,

With a fresh install of Fiji with the new Bioformats release (v6.3.0), it seems that the newly parsed flip options create an error with some Lif Files (that were opening nicely before):

java.lang.NullPointerException
	at loci.formats.in.LIFReader.checkFlip(LIFReader.java:1081)
	at loci.formats.in.LIFReader.initMetadata(LIFReader.java:1038)
	at loci.formats.in.LIFReader.initFile(LIFReader.java:553)
	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)

Here’s the link to a non working lif file:

https://drive.switch.ch/index.php/s/7cg8MFzV806Bh8F

And a link to the related bug fix thread:

Hope that can be easily fixed!

Best,

Nico

1 Like

Thank you @NicoKiaru for the quick feedback as always,

It looks like the support for the flipped/swapped positions discussed in the thread above and introduced in Bio-Formats 6.3.0 broke the reading some variants of the Leica LIF format for which we had no representative sample in our curated QA repository unfortunately.

I confirm the sample file you uploaded is sufficient to reproduce the problem. We will use this file and look into fixing this regression into a upcoming patch release of Bio-Formats. Can the file be made available publicly under the CC-BY license?

4 Likes

Thanks for the fast response, and sure, you can make the file public under CC-BY.

3 Likes

Hi,

Do you have any idea when the fix is supposed to be released ? I need to notify our users when to resume updates on FIJI.

Best,

Nico

Hi Nico, I have opened a PR which should resolve the issue (https://github.com/ome/bioformats/pull/3467). This will be targeted for the next patch release 6.3.1

1 Like

Awesome, thank you very much!