[ome-users] Convert Ariol files (file extension cat)

[Björn Quast]

Hi Andreas

when I look into the file with emacs,  position 118772 appears to be the last 
sign of the xml-header, but there is a line break behind this position. So I 
suggest to try Matthieus solution with offset-value 118774 instead. Worked 
here, but:
In this way you will only find the first tif-image in this file. In archive.xml 
are some BlobSize-values in the node3 structure  that can be added together 
giving the offsets of the next tif-images. 
I think you dont want to search for all this and convert them all by hand,  
isn't there an export to tif-function in your device/database?

best 
Björn


   




> Hi Mathieu,
> I tried your proposed approach but I'm not able to view these images after
> extraction (Ubuntu 64bit). Neither ImageJ nor Gimp were able to open these
> files. Any hints?
> Andreas
> 
> ________________________________________
> Von: Mathieu Malaterre [mathieu.malaterre at dicomstudio.org]
> Gesendet: Montag, 13. Mai 2013 13:53
> An: Andreas Heindl
> Cc: ome-users at lists.openmicroscopy.org.uk
> Betreff: Re: [ome-users] Convert Ariol files (file extension cat)
> 
> 2013/5/13 Andreas Heindl
> <Andreas.Heindl at icr.ac.uk<mailto:Andreas.Heindl at icr.ac.uk>> Dear list,
> 
> I'm puzzled of how to convert slides acquired with Ariol[1] and stored as a
> *.cat file can be converted to a more portable file format such as png or
> jpg. Unfortunately Bio-formats seems not to support this type of file and
> google didn't retrieve possible solutions. Any hints? I also got an example
> files (628MB).
> Greetings,
> Andreas Heindl
> 
> [1]
> http://technoinfo.co.uk/catalog/14.html
> [2]
> https://secure.logmein.com/f?00_dEhcLJtohFR1cODW1QO81Kkbh5v4tBsEENMPzZA6
> 
> 
> At least on UNIX you can extract the TIFF file from the XML header:
> 
> $ cd catExample/POET0002 one
> $ (dd bs=118772 count=1 of=/dev/null && dd bs=4K of=out.tiff ) <
> image.cat<http://image.cat> $ tiffinfo out.tiff
> TIFFReadDirectory: Warning, out.tiff: unknown field with tag 65441 (0xffa1)
> encountered. TIFF Directory at offset 0x1bf88 (114568)
>   Image Width: 2032 Image Length: 2032
>   Bits/Sample: 8
>   Compression Scheme: Deflate
>   Photometric Interpretation: min-is-black
>   Samples/Pixel: 1
>   Rows/Strip: 4
>   Planar Configuration: single image plane
>   ImageDescription: Red 1.25X
>   Tag 65441: 46198
> TIFFReadDirectory: Warning, out.tiff: unknown field with tag 65441 (0xffa1)
> encountered. TIFF Directory at offset 0x40008 (262152)
>   Image Width: 2032 Image Length: 2032
>   Bits/Sample: 8
>   Compression Scheme: Deflate
>   Photometric Interpretation: min-is-black
>   Samples/Pixel: 1
>   Rows/Strip: 4
>   Planar Configuration: single image plane
>   ImageDescription: Green 1.25X
>   Tag 65441: 177402
> TIFFReadDirectory: Warning, out.tiff: unknown field with tag 65441 (0xffa1)
> encountered. TIFF Directory at offset 0x64fd4 (413652)
>   Image Width: 2032 Image Length: 2032
>   Bits/Sample: 8
>   Compression Scheme: Deflate
>   Photometric Interpretation: min-is-black
>   Samples/Pixel: 1
>   Rows/Strip: 4
>   Planar Configuration: single image plane
>   ImageDescription: Blue 1.25X
>   Tag 65441: 327052
> 
> HTH
> 
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-- 
Dr. Björn Quast
Universität Bonn
Institut für Evolutionsbiologie und Ökologie
An der Immenburg 1
53121 Bonn
Tel.: 0228/735758   email: bquast at evolution.uni-bonn.de