error with opening 16 bit LSM files

[kbseah]

Hello:

I've been using ImageJ to work with LSM files for some time with no problem.
However, when I recently tried to open a 16 bit LSM file (which I'd opened
with no issues before), it gave me this output instead (attached image).

As you can see the top bar says that it's a 8 bit file, but it was
originally saved as a 16 bit file. I've opened a few other files and some
work, while others don't.

I'm using version 1.44, but the same issue comes up in 1.41.

Has anyone seen this before and know how to fix it? Could the image files be
corrupted?

Thanks a lot!
Brandon Seah

[ctrueden]

Hi Brandon,

There are (at least) two ways to read LSM files into ImageJ: the built-in
LSM reader plugin, and the Bio-Formats plugin (
http://www.loci.wisc.edu/bio-formats/imagej). Do you see the same results
with both?

If one works but the other doesn't, it may be a bug in the non-working
reader. Otherwise, it is likely (but not necessarily) a problem with your
file.

-Curtis

On Tue, Aug 30, 2011 at 3:51 AM, Brandon Seah <[hidden email]> wrote:

> Hello:
>
> I've been using ImageJ to work with LSM files for some time with no
> problem.
> However, when I recently tried to open a 16 bit LSM file (which I'd opened
> with no issues before), it gave me this output instead (attached image).
>
> As you can see the top bar says that it's a 8 bit file, but it was
> originally saved as a 16 bit file. I've opened a few other files and some
> work, while others don't.
>
> I'm using version 1.44, but the same issue comes up in 1.41.
>
> Has anyone seen this before and know how to fix it? Could the image files
> be
> corrupted?
>
> Thanks a lot!
> Brandon Seah
>

[kbseah]

Thanks Curtis! I installed BioFormats and installed the latest version of
LSM reader and both work fine now.

-Brandon

On Tue, Aug 30, 2011 at 10:10 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Brandon,
>
> There are (at least) two ways to read LSM files into ImageJ: the built-in
> LSM reader plugin, and the Bio-Formats plugin (
> http://www.loci.wisc.edu/bio-formats/imagej). Do you see the same results
> with both?
>
> If one works but the other doesn't, it may be a bug in the non-working
> reader. Otherwise, it is likely (but not necessarily) a problem with your
> file.
>
> -Curtis
>
> On Tue, Aug 30, 2011 at 3:51 AM, Brandon Seah <[hidden email]> wrote:
>
> > Hello:
> >
> > I've been using ImageJ to work with LSM files for some time with no
> > problem.
> > However, when I recently tried to open a 16 bit LSM file (which I'd
> opened
> > with no issues before), it gave me this output instead (attached image).
> >
> > As you can see the top bar says that it's a 8 bit file, but it was
> > originally saved as a 16 bit file. I've opened a few other files and some
> > work, while others don't.
> >
> > I'm using version 1.44, but the same issue comes up in 1.41.
> >
> > Has anyone seen this before and know how to fix it? Could the image files
> > be
> > corrupted?
> >
> > Thanks a lot!
> > Brandon Seah
> >
>