Bioformats Importer Issue

Hey everyone,

I’m having an issue with using the Bioformats importer loading an z-stack. It’s always worked in the past, but the last two updates I’ve gotten to Bioformats seem to result in an error when I try to import a stack.

Is anyone having the same issue? or any advice on how to fix it before I try to rerun a clean instance of FIJI?

-Wilson

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 323MB of 49012MB (<1%)
 
java.lang.NullPointerException
	at loci.formats.in.APLReader.isThisType(APLReader.java:98)
	at loci.formats.ImageReader.getReader(ImageReader.java:188)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:620)
	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.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:63)
	at ij.IJ.run(IJ.java:309)
	at ij.IJ.run(IJ.java:320)
	at ij.macro.Functions.doRun(Functions.java:623)
	at ij.macro.Functions.doFunction(Functions.java:97)
	at ij.macro.Interpreter.doStatement(Interpreter.java:270)
	at ij.macro.Interpreter.doBlock(Interpreter.java:666)
	at ij.macro.Interpreter.runMacro(Interpreter.java:179)
	at ij.macro.MacroRunner.run(MacroRunner.java:152)
	at java.lang.Thread.run(Thread.java:748)

Hi @Wilson_Adams, are the files you are trying to read located in the root folder? Moving them up into a higher directory will likely solve the issue. This is something which are looking into fixing: https://github.com/openmicroscopy/bioformats/issues/3343

1 Like

Hi @dgault,

They are located on a nearby server, not in the root folder. It seems to work fine on one of my other machines, but two of my machines keep throwing this error.

I experience that error if the images are in a directory one down from the root… which makes sense from the code snippet I posted in the issue (since the parent file is requested three times). Moving the images into another further sub-directory resolved the issue.

1 Like

I think i solved the issue. It was one of many issues I was having for some reason (Autocompletion not working, some plugin functionality lost).

Uninstalling and reinstalling a fresh Fiji-Legacy through the updater fixed everything.

Thanks to @dgault and @petebankhead for your timely response