Posted by
Philip Ershler on
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-file-defeats-LSM-Reader-Toolbox-tp3697026p3697027.html
On Mar 4, 2008, at 2:47 AM, 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?
>
I ran into this same issue. The problem is that when the two gentlemen
wrote the LSM ToolBox, they had no line scan files (scantype: 2) to test
their software. So rather than push out some software that might give
unreliable results, they excluded line scan files. After I sent them
several
examples linescan files, they modified the ToolBox so that it can now
handle linescan files. I'm not sure if the changed Toolbox is
available for
download from the ImageJ web site. Check there first and make sure
that you've got the most recent version of ImageJ and the LSM Toolbox.
Actually, the LSM Reader has been folded into the ImageJ program. This
means that one can open LSM files right from the File Menu.
If you can't get a version of something that will open your linescan
files, get back to me and I will send you a copy of what I've got.
HTH,
Phil