opening obi files in imagej with bio-formats fails

[pkingsley]

Hello OME forum members,
I am trying to open obi files in imagej and I downloaded the bioformats plugins. Inside ImageJ>plugins, I have loci_tools.jar and ome_plugins.jar. I go to the plugins menu, then LOCI, then bio formats importer. I then navigate to a simple obi file, use default parameters, and generate a list of errors that I have pasted below. Any thoughts as to what I may be doing wrong?

ImageJ 1.47v; Java 1.6.0_65 [64-bit]; Mac OS X 10.7.5; 12MB of 658MB (1%)

java.lang.NullPointerException
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:520)
at loci.formats.FormatReader.setId(FormatReader.java:213)
at loci.plugins.Importer.run(Importer.java:172)
at loci.plugins.LociImporter.run(LociImporter.java:74)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:128)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)

[mlinkert]

If you select "Help > About Plugins > LOCI Plugins" in ImageJ, which version number and date are shown?

[pkingsley]

Thank-you for taking the time to respond to my post. "LOCI Plugins for ImageJ, built 5 August 2008
That does seem a while ago, but I believe I downloaded them yesterday…

[mlinkert]

Yes, that's a very old version - the latest stable version is 4.4.9, dated 16 October 2013.

Did you download loci_tools.jar from here: http://downloads.openmicroscopy.org/bio-formats/4.4.9/ ? If so, please make sure that there aren't any other files with names similar to loci_tools.jar or loci_plugins.jar in your ImageJ plugins folder.

[pkingsley]

Dear mlinkert,
Thanks for continuing to help me. I feel I am doing something very very simple incorrectly. I did download those files, In my ImageJ>plugins> are a couple of jar folders loci_tools.jar and one_plugins.jar The loci_tools.jar is a Java JAR file created 9-12-13. Yet when I run ImageJ (or ImageJ 64 bit), band do the get info ion plugins, I still get LOCI Plugins for ImageJ, built 5 August 2008. When I search my computer for any file that contains the text loci in its name, that is the only result that matches. Somewhere, there is another JAR that is being read, but I don't know where it is, or where I should put the correct JAR file

[mlinkert]

The attached image unfortunately doesn't display. Probably the easiest thing to do is to create a Zip file that contains your ImageJ installation and upload it to:

http://qa.openmicroscopy.org.uk/qa/upload/

We can then see exactly what's going wrong, and give you more accurate guidance on how to solve it.

[pkingsley]

I have uploaded the file imagej kingsley.zip

Perhaps a simpler strategy would be for me to uninstall and reinstall imageJ?

[mlinkert]

Thank you for uploading the screenshot. There isn't anything obvious from the screenshot, but it doesn't show the entire contents of the plugins folder.

Reinstalling ImageJ would certainly work; if you don't want to do that, then please upload a Zip file that contains the entire contents of your current ImageJ folder and we'll find out the problem from there.

[pkingsley]

Thank you for being patient with me. I did not realize you wanted not just the plugin folder contents, but the subfolder contents as well, obvious, I guess. I have uploaded a second zip file with three screenshots that cover the imagej plugin contents, and subfolder contents.

[mlinkert]

Could you please try completely removing loci_tools.jar, download it again and then verify that the file size is correct? Version 4.4.9 of loci_tools.jar should be 10001340 bytes (~9.6 MB); as shown in the screenshot, it is substantially smaller than it should be.