Re: 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-tp3697026p3697030.html

Michael,

Whether I like it or not, I have to work with the files that my colleagues
produce. I could ask them to turn off compression (if there's a switch) but
they may not do that if the increase in file size makes the files unwieldy
e.g. they can't burn one experiment onto a DVD disc.

Francis

At 10:53 04/03/08 +0100, you wrote:

>Francis,
>
>why do you use the Zeiss compression? This only makes things more difficult.
>
>Michael
>
>
>Francis Burton wrote:
>> 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
>
>