[ome-users] [micro-manager-general] Bug: LOCI Bio-Formats importer doesn't like MM OME tiffs
Melissa Linkert
melissa at glencoesoftware.com
Tue Mar 26 23:53:52 GMT 2013
Hi Brian,
> - The third behavior, black images opened after saving a
> multi-dimensional acquisition as a set of individual files (one for each
> image), is still present. They open fine using ImageJ's regular "Open"
> command. I'll upload a sample tarball to the OpenMicroscopy website.
Thank you for uploading a dataset. This is a bug in Bio-Formats, and so
there is now a ticket on OME's issue tracking system to fix it:
http://trac.openmicroscopy.org.uk/ome/ticket/10610
You have been CC'd on that ticket, and so will be notified of any
updates. If you prefer not to be notified, please let me know.
Regards,
-Melissa
On Mon, Mar 25, 2013 at 01:41:56PM -0400, Brian Teague wrote:
> Melissa and Henry (and two whole mailing lists worth of lookers-on)
>
> Thanks for your feedback. Henry Pinkard, one of the Micro-Manager devs,
> replied off-list; I'll repeat/summarize.
>
> - The first behavior, an exception when opening images snapped from a
> live camera view and saved as an image stack, was a bug and is now fixed
> (I confirmed it with last night's nightly.)
>
> - The second behavior, saving a multi-dimensional acquisition as a set
> of image stacks, isn't a bug. Even though each position in the multi-d
> acquisition is saved to a separate file, Bio-Formats treats the entire
> acquisition as a single logical entity. So, if I use the regular
> Bio-Formats importer, no matter which of the files I open, I'm asked
> which series I wish to open from the entire data set. If I use the
> "windowless" importer, it just opens the first series, again regardless
> of which file I select in the Open... dialog box. This is the intended
> behavior.
>
> - The third behavior, black images opened after saving a
> multi-dimensional acquisition as a set of individual files (one for each
> image), is still present. They open fine using ImageJ's regular "Open"
> command. I'll upload a sample tarball to the OpenMicroscopy website.
>
> Thanks for your help.
> Brian
>
> On Fri, 2013-03-22 at 13:34 -0400, Melissa Linkert wrote:
> > Hi Brian,
> >
> > [CC'ing the ome-users mailing list, as that is the best place to
> > report Bio-Formats issues.]
> >
> > > I've run into a problem opening OME TIFFs saved by Micro-Manager with
> > > the LOCI Bio-Formats importer. If I just use the plain ImageJ "Open"
> > > command, things work as expected, but if I use Bio-Formats importer in
> > > Fiji, I have various problems depending on how I saved the files in MM:
> >
> > First, please make sure that you have the latest version of Bio-Formats
> > installed in ImageJ. "Help > About Plugins > LOCI Plugins" will tell you the
> > version and date; 4.4.6 is the latest.
> >
> > If updating doesn't solve the problem, then it would be useful if you could
> > upload a small number of files that demonstrate the problem(s). You can upload
> > files here:
> >
> > http://qa.openmicroscopy.org.uk/qa/upload/
> >
> > If uploading there doesn't work, I can send alternate instructions privately.
> >
> > Regards,
> > -Melissa
> >
> > On Fri, Mar 22, 2013 at 12:07:28PM -0400, Brian Teague wrote:
> > > MM Devs -
> > >
> > > First, thanks for a great piece of software (and congrats on the new
> > > release!) It has really enabled the kind of workflow that lets me get
> > > some solid experiments done.
> > >
> > > I've run into a problem opening OME TIFFs saved by Micro-Manager with
> > > the LOCI Bio-Formats importer. If I just use the plain ImageJ "Open"
> > > command, things work as expected, but if I use Bio-Formats importer in
> > > Fiji, I have various problems depending on how I saved the files in MM:
> > >
> > > - If I "snap" a set of live-view images into an album, I get an
> > > ArrayIndexOutOfBoundsException:
> > >
> > > Caused by: java.lang.ArrayIndexOutOfBoundsException: 2
> > > at
> > > loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:633)
> > > at loci.formats.FormatReader.setId(FormatReader.java:1333)
> > > at
> > > loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> > > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> > > at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> > > at loci.plugins.in.Importer.run(Importer.java:79)
> > > at loci.plugins.LociImporter.run(LociImporter.java:81)
> > > at ij.IJ.runUserPlugIn(IJ.java:193)
> > > at ij.IJ.runPlugIn(IJ.java:160)
> > > ... 7 more
> > >
> > > - If I do a Multi-D acquisition (4 positions) and save as multi-image
> > > files, I get a file per position; but when I try to open one of the
> > > files, the default Bio-Formats importer allows me to choose to open any
> > > of the images in the acquisition; and the "windowless" importer simply
> > > opens the first position regardless of which file I choose.
> > >
> > > - If I do a Multi-D acquisition (4 positions) but save as single-image
> > > files instead, I get a black image. (And yes, it's actually black, not
> > > just a 12-bit image in a 16-bit space)
> > >
> > > The reason I need to use the Bio-Formats importer instead of just
> > > opening in ImageJ/Fiji directly is because I'm using MM's grid
> > > acquisition feature to make large mosaics, then stitching them back
> > > together to analyze using Fiji's excellent Grid/Collection Stitching
> > > plugin. The Stitching plugin uses the Bio-Formats importer, performing
> > > the equivalent of a "Windowless Import" on each file specified.
> > >
> > > My current workaround is to batch "convert" the files, re-saving them as
> > > ImageJ TIFFs, then stitching - but it's getting to be kind of a pain.
> > >
> > > I've looked for configuration options (both in MM and Bio-Formats) but
> > > haven't found any that affect the bug. I guess it's also possible that
> > > it's a Bio-Formats bug - I'll file one with LOCI if you thing that's the
> > > case.
> > >
> > > Finally, I'm happy to provide sample images, though reproducing locally
> > > should be no challenge. I can't imagine that it's a hardware-specific
> > > bug, but if it is, my setup is:
> > > - a Zeiss 200M stand
> > > - an Axiocam MRm v.2 camera
> > >
> > > Thanks in advance,
> > > Brian
> > >
> > > --
> > > Brian Teague
> > > teague at mit.edu
> > > Weiss Group, Synthetic Biology Center @ MIT
> >
> >
> >
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> >
>
>
> --
> Brian Teague
> teague at mit.edu
> Weiss Group, Synthetic Biology Center @ MIT
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