[ome-users] [micro-manager-general] Bug: LOCI Bio-Formats importer doesn't like MM OME tiffs

[Melissa Linkert]

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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