[ome-devel] ADF images of BD Pathway Bioimager

[Jason H]

Hi Melissa,

Thanks for the message.

> Bio-Formats does have support for BD Pathway data, but you will need
> to use a recent trunk build as this format was added after the last

I managed to build loci_tools.jar from the source code in the trunk a few
days ago.  With this new loci_tools.jar, bfconvert still gives an error when
a .adf file is fed to it.  Maybe this is because those .adf files are not images
at all, as implied by the message from Shawn?

> stable release.  It's important to note that Bio-Formats' BD reader
> currently does not allow you to choose the *.adf files; you must
> choose the 'Experiment.exp' file in order for the dataset to be

What program do I have to use to choose this Experiment.exp file?  ImageJ?
With the new loci_tools.jar and ImageJ, selecting an Experiment.exp file with
Plugins > LOCI > Bio-Formats Importer just gives me a window displaying the
following message:
java.lang.NullPointerException
at loci.common.Location.getHandle(Location.java:183)
at loci.common.Location.getHandle(Location.java:167)
at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:71)
at loci.common.DataTools.readFile(DataTools.java:55)
at loci.formats.in.BDReader.parseROIs(BDReader.java:497)
at loci.formats.in.BDReader.initFile(BDReader.java:340)
at loci.formats.FormatReader.setId(FormatReader.java:1000)
at loci.plugins.importer.ImporterReader.prepareStuff(ImporterReader.java:100)
at loci.plugins.importer.ImporterOptions.showDialogs(ImporterOptions.java:221)
at loci.plugins.importer.Importer.showOptionDialogs(Importer.java:116)
at loci.plugins.importer.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:77)
at ij.IJ.runUserPlugIn(IJ.java:175)
at ij.IJ.runPlugIn(IJ.java:142)
at ij.Executer.runCommand(Executer.java:121)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Thread.java:619)

I guess I did something wrong most likely.

> correctly detected.  If it would be useful to you, we can update the
> reader to allow the *.adf files to be selected.

Thank you very much for the offer.  It's OK to leave it alone as is.

Best wishes,

Jason