[ome-devel] ADF images of BD Pathway Bioimager

[Shawn Garbett]

On Apr 29, 2010, at 12:39 PM, Jason H 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?

Should use the OMERO Importer.

> 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.

This looks like an error in the package. The problem I had in developing is I have access to a single BD Pathway, the BD software you have may be doing something different. Would it be possible to get a small test dataset via ftp or mailing a CDROM from your machine?

> 
>> 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.

Okay.

Shawn Garbett <shawn.p.garbett at vanderbilt.edu>
Vanderbilt Cancer Biology
220 Pierce Ave, PRB 715AA
Nashville, TN 37232
Office: 615.936.1975
Cell: 615.397.8737