Open Microscopy Environment

Hello,
I am trying to open a Kodak .bip file through ImageJ Bio-Formats plug-in, however I am having no luck. Has anyone else successfully opened this type of file before? Thanks!

Here is my error:

Code: Select all

java.lang.StringIndexOutOfBoundsException: String index out of range: -1
   at java.lang.String.substring(String.java:1937)
   at loci.formats.in.KodakReader.readExtraMetadata(KodakReader.java:183)
   at loci.formats.in.KodakReader.initFile(KodakReader.java:120)
   at loci.formats.FormatReader.setId(FormatReader.java:1072)
   at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
   at loci.plugins.in.Importer.showDialogs(Importer.java:125)
   at loci.plugins.in.Importer.run(Importer.java:77)
   at loci.plugins.LociImporter.run(LociImporter.java:79)
   at ij.IJ.runUserPlugIn(IJ.java:183)
   at ij.IJ.runPlugIn(IJ.java:150)
   at ij.Executer.runCommand(Executer.java:127)
   at ij.Executer.run(Executer.java:64)
   at java.lang.Thread.run(Thread.java:680)


Hi,

I am trying to open a Kodak .bip file through ImageJ Bio-Formats plug-in, however I am having no luck. Has anyone else successfully opened this type of file before?

From the error message, it looks like you might have a slightly outdated version of Bio-Formats installed. Could you please try updating to the latest trunk build and see if that solves the problem?

If the file still does not open after updating, then it would be very helpful if you could send an example .bip file, as all of the files that we have here do open correctly. If you need somewhere to upload files, please let me know and I will send you our SFTP server information.

Regards,
-Melissa

Thank you for your fast reply Melissa!!!

Here is some background info of what I used to produce the .bip file below:
-Kodak Image Station 440 CF
-Kodak Molecular Imaging Software, Network version 4.0.5

Tried opening .bip from ImageJ 1.45S by:
-File ->Import->Bio-Formats
Here of my screenshot of the next step:


Downloaded the latest Trunk build at 11:10pm EST 2/28/12 from "http://loci.wisc.edu/bio-formats/downloads". Next, placed file in "plugins" folder.

Here is the .bip
http://dl.dropbox.com/u/23809996/1.bip

Thank you for any help!

Hi,

Thank you very much for sending an example file. We have implemented a fix, described here:

https://github.com/melissalinkert/biofo ... 96c321c5b3

The next trunk build of Bio-Formats (and the next stable version) will contain this fix.

Regards,
-Melissa

Melissa, you rock.

How often do trunk builds come out?

How often do trunk builds come out?

A new trunk build is generated whenever a set of changes has passed review by the rest of the team. The time between builds varies quite a bit, but 1-2 weeks is fairly average at this point.

Regards,
-Melissa

Thanks Melissa. Sorry to bother you again but just as a temporary fix I went ahead and edited the following in the .bip file so that I can open it with ImageJ Bio-Formats:

Code: Select all

   
Vertical Resolution: 113 mm                     
Horizontal Resolution: 111 mm      


Now the .bip opens but it is black and no matter what I do or try nothing can reveal the bands that should be present.

Thanks for any help

Sorry to bother you again but just as a temporary fix I went ahead and edited the following in the .bip file so that I can open it with ImageJ Bio-Formats:

Code: Select all

   
Vertical Resolution: 113 mm                     
Horizontal Resolution: 111 mm     


That makes sense, though I would advise against doing that to all of your files!

Now the .bip opens but it is black and no matter what I do or try nothing can reveal the bands that should be present.

This was just fixed:

https://github.com/melissalinkert/biofo ... 497c0f8930

Regards,
-Melissa

It's working now!!! For years I have waited for this moment! awesome x10^∞