*.stk files from AutoQuant - problem opening in ImageJ or LOCI

[Graham Wright]

Dear Listers,

I have some files generated after deconvolution with AutoQuant and am
having trouble opening them with ImageJ (thay can be opened fine in
MetaMorph or back in AutoQuant). So, i'm hoping for some help.

The original raw data (MetaMorph generated stk) can be opened
perfectly well with ImageJ, either by dragging the file onto the
ImageJ window or by opening it through the LOCI Bioformats importer
(old version - downlaoded Jan '08). The new version of LOCI
(downloaded today - v4.0.0) opens the first image in the stack then
slices 2-13 are all slice 2.

The deconvolved data cannot be opened by any of the above options.
Dragging it onto the ImageJ window only opens the first slice of the
stack. The new LOCI has the same problem as with the raw data. Going
through the old LOCI give the following exception:

java.lang.ArrayIndexOutOfBoundsException: 0
        at loci.formats.TiffTools.getSamples(TiffTools.java:1446)
        at loci.formats.in.BaseTiffReader.openBytes(BaseTiffReader.java:144)
        at loci.formats.in.MetamorphReader.openBytes(MetamorphReader.java:147)
        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:156)
        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:165)
        at loci.plugins.Util.openProcessor(Util.java:80)
        at loci.plugins.Importer.run(Importer.java:414)
        at loci.plugins.LociImporter.run(LociImporter.java:74)
        at ij.IJ.runUserPlugIn(IJ.java:177)
        at ij.IJ.runPlugIn(IJ.java:143)
        at ij.Executer.runCommand(Executer.java:121)
        at ij.Executer.run(Executer.java:58)
        at java.lang.Thread.run(Unknown Source)

Any help will be much appreciated.

Thanks,
Graham

-----
Graham Wright
Microscopy & Imaging Facility

Temasek Life Sciences Laboratory
1 Research Link
National University of Singapore
Singapore 117604

P:    [phone]
E:     [hidden email]
W:    http://microscopy.tll.org.sg

[ctrueden]

Hi Graham,

Would you be willing to send us some example non-working datasets? Files
less than 15 MB can be emailed directly to the Bio-Formats email address
(see http://www.loci.wisc.edu/ome/formats-contact.html); if your files are
larger let us know and I will send you our FTP server information off-list.

Thanks,
Curtis

On Wed, May 20, 2009 at 10:34 AM, Graham Wright <
[hidden email]> wrote:

> Dear Listers,
>
> I have some files generated after deconvolution with AutoQuant and am
> having trouble opening them with ImageJ (thay can be opened fine in
> MetaMorph or back in AutoQuant). So, i'm hoping for some help.
>
> The original raw data (MetaMorph generated stk) can be opened
> perfectly well with ImageJ, either by dragging the file onto the
> ImageJ window or by opening it through the LOCI Bioformats importer
> (old version - downlaoded Jan '08). The new version of LOCI
> (downloaded today - v4.0.0) opens the first image in the stack then
> slices 2-13 are all slice 2.
>
> The deconvolved data cannot be opened by any of the above options.
> Dragging it onto the ImageJ window only opens the first slice of the
> stack. The new LOCI has the same problem as with the raw data. Going
> through the old LOCI give the following exception:
>
> java.lang.ArrayIndexOutOfBoundsException: 0
>        at loci.formats.TiffTools.getSamples(TiffTools.java:1446)
>        at loci.formats.in.BaseTiffReader.openBytes(BaseTiffReader.java:144)
>        at
> loci.formats.in.MetamorphReader.openBytes(MetamorphReader.java:147)
>        at
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:156)
>        at
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:165)
>        at loci.plugins.Util.openProcessor(Util.java:80)
>        at loci.plugins.Importer.run(Importer.java:414)
>        at loci.plugins.LociImporter.run(LociImporter.java:74)
>        at ij.IJ.runUserPlugIn(IJ.java:177)
>        at ij.IJ.runPlugIn(IJ.java:143)
>        at ij.Executer.runCommand(Executer.java:121)
>        at ij.Executer.run(Executer.java:58)
>        at java.lang.Thread.run(Unknown Source)
>
> Any help will be much appreciated.
>
> Thanks,
> Graham
>
> -----
> Graham Wright
> Microscopy & Imaging Facility
>
> Temasek Life Sciences Laboratory
> 1 Research Link
> National University of Singapore
> Singapore 117604
>
> P:    [phone]
> E:     [hidden email]
> W:    http://microscopy.tll.org.sg
>