[ome-users] [micro-manager-general] Bug: LOCI Bio-Formats importer doesn't like MM OME tiffs
Brian Teague
teague at MIT.EDU
Mon Mar 25 17:41:56 GMT 2013
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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