Zeiss LSM file defeats LSM Reader & Toolbox

Posted by Francis Burton on
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-file-defeats-LSM-Reader-Toolbox-tp3697026.html

Hi,

I'm trying to read Zeiss LSM files directly into ImageJ rather than having
to use the free Zeiss Image Browser software to export TIFFs first. These
files are produced from linescan experiments (laser whizzes back and forth
along a line, resulting in an image representing x vs time). There are two
12 bit channels, one for each wavelength used, and the resulting 'images'
are subsequently ratioed to produce a single linescan image.

Unfortunately, none of the available free software that I have tried so far
seems to be able to handle these files. LSM Reader reports "Unsupported LSM
scantype: 2", and if I rename the file from .LSM to .TIF, TiffDecoder tells
me that "ImageJ cannot open 48-bit LZW compressed TIFFs".

(I also tried the MATLAB function tiffread.m mentioned at
http://en.wikipedia.org/wiki/LSM_(Zeiss) but that didn't work either and
in any case I really want to use ImageJ not MATLAB!)

Would it be straightforward to modify LSM Reader to be able to handle these
files? Presumably a LZW decoder is now included. Is it simply a matter of
interpreting the resulting decompressed bytes as pairs of 12 bit chunks?

Cheers,
Francis

--
Dr Francis L Burton,          |  [hidden email]
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