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

[Andreas Heindl]

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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