[ome-devel] ADF images of BD Pathway Bioimager

[Melissa Linkert]

Hi Jason,

> What program do I have to use to choose this Experiment.exp file?  ImageJ?

Bio-Formats, in any of it's applications.  Using ImageJ is a fine way
to make sure the dataset opens correctly, but you could also use any
of the other applications listed here (as long as Bio-Formats is
properly installed):

http://loci.wisc.edu/bio-formats/applications

> 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:

This was a problem with some ROI parsing code that I added to Shawn's
original BD reader.  The very latest trunk build should fix it.

If you continue to notice problems, then as Shawn mentioned it would
help if you could make one of your datasets available.

Regards,
-Melissa

On Thu, Apr 29, 2010 at 12:39 PM, Jason H <qz8w9l at gmail.com> wrote:
> 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
>