Bio-Formats won't open .OIF files

I’m trying to load some .oif files on Fiji but keep getting this error.

java.io.FileNotFoundException: C:\Users\tamcd\Downloads\Images\Male DRG 1 hrs 1 uM NCLS pACC-periph 1 Tim.oif.files\s_C001.pty (The system cannot find the path specified)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.(RandomAccessFile.java:243)
at loci.common.NIOFileHandle.(NIOFileHandle.java:130)
at loci.common.Location.getHandle(Location.java:412)
at loci.common.RandomAccessInputStream.(RandomAccessInputStream.java:138)
at loci.formats.in.FV1000Reader.getFile(FV1000Reader.java:1647)
at loci.formats.in.FV1000Reader.getIniFile(FV1000Reader.java:1755)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:687)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
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:228)
at ij.IJ.runPlugIn(IJ.java:192)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)

Good day,

I guess the problem is with the file name of your image.

It contains several blanks and perhaps some problematic chars.

Maybe you rename the file and try again.

Good luck

Herbie

I tried deleting all of the spaces. It’s giving the same error message

Hi there,

I’m running into the same problem, were you able to find a solution?

Thanks!

Hi @jt115, is it the same error message (FileNotFoundException) and stack trace you are seeing?

Hi @dgault

Yes, I’m getting the same error message, but the stack trace is slightly different:

java.io.FileNotFoundException: C:\Users\Jacob Tharayil\Downloads\CUS2 IL. (60x).oif.files\s_C001Z001.pty (The system cannot find the file specified)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.(RandomAccessFile.java:243)
at loci.common.NIOFileHandle.(NIOFileHandle.java:130)
at loci.common.Location.getHandle(Location.java:518)
at loci.common.RandomAccessInputStream.(RandomAccessInputStream.java:138)
at loci.formats.in.FV1000Reader.getFile(FV1000Reader.java:1642)
at loci.formats.in.FV1000Reader.getIniFile(FV1000Reader.java:1750)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:682)
at loci.formats.FormatReader.setId(FormatReader.java:1392)
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:235)
at ij.IJ.runPlugIn(IJ.java:198)
at ij.Executer.runCommand(Executer.java:150)
at ij.Executer.run(Executer.java:68)
at java.lang.Thread.run(Thread.java:745)

Hope this helps!

Do you see the same error with all your OIF files or is it only a particular fileset?

Just to test a few possibilities, would you be able to rename the following the see if helps as a temporary workaround:

  • Rename the folder to remove the brackets
  • Rename the folder to remove the . period char