Re: Zeiss LSM file defeats LSM Reader & Toolbox

Posted by Patrick Pirrotte on
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-file-defeats-LSM-Reader-Toolbox-tp3697026p3697028.html

Hi,

I've got one bug I'd like to squash before releasing the LSMToolbox/LSMReader 4.0c.
I'll try to do that still this week and release the new version.

Regards,

Patrick

----- Original Message -----
From: Philip Ershler <[hidden email]>
Date: Tuesday, March 4, 2008 23:02
Subject: Re: Zeiss LSM file defeats LSM Reader & Toolbox
To: [hidden email]

> 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
>