Re: Zeiss LSM file defeats LSM Reader & Toolbox

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-file-defeats-LSM-Reader-Toolbox-tp3697026p3697029.html

Hi Francis,

Did you try Bio-Formats? http://www.loci.wisc.edu/ome/formats.html

-Curtis

On Tue, Mar 4, 2008 at 3:47 AM, Francis Burton <[hidden email]>
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)<http://en.wikipedia.org/wiki/LSM_%28Zeiss%29>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]
> West Medical Building,        |
> University of Glasgow,        |  Tel [phone]
> Glasgow, G12 8QQ, Scotland.   |  Fax [phone]
>