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

[Daniel James White]

Hi Graham,

Try another file format as a work around.
I find that the ics / ids files autoquant writes seem to work ok.

Dan



On May 21, 2009, at 6:00 AM, IMAGEJ automatic digest system wrote:

>
> Date:    Wed, 20 May 2009 16:34:48 +0800
> From:    Graham Wright <[hidden email]>
> Subject: *.stk files from AutoQuant - problem opening in ImageJ or  
> LOCI
>
> 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

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de Fiji Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )