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Problems reading LSM files

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Ronald Steffen

Problems reading LSM files

Hi all,

I just installed ImageJ (Ver. 1.39u) and the LSM Toolbox (Ver. 4.0c). When I
try to read my Zeiss 510 Meta 12 bit lsm-files the read images or stacks are
corrupted.

There's only bit-noise, the lower part of the images is black and stacks
have about half the number of frames. This is the same whether I use ImageJ
or LSM Toolbox to read the files. The preview in the Open LSM dialog shows a
2x2 tiled version of the original uncorrupted image. There seems to be an
issue with recognizing the file header.

Does anyone have the same problem and a solution? I seem to have installed
the latest software versions but the microscope was purchased rather
recently (within the last 6 month). Did they modify there files formats
again?

I'm grateful for any suggestions.

Cheers,

Ronald

Michael Weber-4

Re: Problems reading LSM files

Ronald,

sounds strange, current 12bit LSM stacks work fine on my side with
standard ImageJ 1.40 LSM support. Did you try the LOCI BioFormats Reader
for import? This might help to figure out where the problem comes from.

Michael

Ronald Steffen wrote:

> Hi all,
>
>
>
> I just installed ImageJ (Ver. 1.39u) and the LSM Toolbox (Ver. 4.0c). When I
> try to read my Zeiss 510 Meta 12 bit lsm-files the read images or stacks are
> corrupted.
>
> There's only bit-noise, the lower part of the images is black and stacks
> have about half the number of frames. This is the same whether I use ImageJ
> or LSM Toolbox to read the files. The preview in the Open LSM dialog shows a
> 2x2 tiled version of the original uncorrupted image. There seems to be an
> issue with recognizing the file header.
>
> Does anyone have the same problem and a solution? I seem to have installed
> the latest software versions but the microscope was purchased rather
> recently (within the last 6 month). Did they modify there files formats
> again?
>
> I'm grateful for any suggestions.
>
>
>
> Cheers,
>
> Ronald

Wayne Rasband

Re: Problems reading LSM files

In reply to this post by Ronald Steffen

> I just installed ImageJ (Ver. 1.39u) and the LSM Toolbox (Ver. 4.0c).
> When I
> try to read my Zeiss 510 Meta 12 bit lsm-files the read images or
> stacks are
> corrupted.
>
> There's only bit-noise, the lower part of the images is black and
> stacks
> have about half the number of frames. This is the same whether I use
> ImageJ
> or LSM Toolbox to read the files. The preview in the Open LSM dialog
> shows a
> 2x2 tiled version of the original uncorrupted image. There seems to be
> an
> issue with recognizing the file header.
>
> Does anyone have the same problem and a solution? I seem to have
> installed
> the latest software versions but the microscope was purchased rather
> recently (within the last 6 month). Did they modify there files formats
> again?

Try upgrading to ImageJ 1.40d using the Plugins>Utilities>Upgrade
ImageJ command. ImageJ 1.39 has a bug that causes reading of some LZW
compressed files to fail.

-wayne

Ronald Steffen

Re: Problems reading LSM files

Hi Carlos, Michael and Wayne,

Thank you for your help. Unfortunately I wasn't able to update to version
1.40. The update feature was "Unable to open release notes at
http://rsb.info.nih.gov/ij/notes.html" and didn't update the software. On
the ImageJ web-page I only found version 1.39.
However, the LOCI BioFormats Reader eventually did the job. It correctly
reads all images and stacks.

Thanks a lot,
Ronald

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne
Rasband
Sent: 11 April 2008 16:17
To: [hidden email]
Subject: Re: Problems reading LSM files

Try upgrading to ImageJ 1.40d using the Plugins>Utilities>Upgrade
ImageJ command. ImageJ 1.39 has a bug that causes reading of some LZW
compressed files to fail.

-wayne

Joachim Wesner

Manual upgrading - Was: Re: Problems reading LSM files

> Hi Carlos, Michael and Wayne,
>
> Thank you for your help. Unfortunately I wasn't able to update to version
> 1.40. The update feature was "Unable to open release notes at
> http://rsb.info.nih.gov/ij/notes.html" and didn't update the software. On
> the ImageJ web-page I only found version 1.39.

You can always upgrade using the good old JAR download method described on

http://rsb.info.nih.gov/ij/upgrade/

which means "manually" copying the new ij.jar to the the ImageJ folder.

(However, the new (built-in) plugin makes things soo much easier - if your
version if new enough to use it)

Joachim

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Ronald Steffen

Re: Manual upgrading - Was: Re: Problems reading LSM files

Hi Joachim,

Thanks for that. I'm now on version 1.40d. Unfortunately there still seems
to be an issue in the new version. File/Open and LSM Toolbox now correctly
read some single channel lsm-files. For stacks the correct number of images
is read but the images are all black (numeric values <= 35).
Good I have the LOCI imported stack for comparison ...

Thanks,
Ronald

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Joachim Wesner
Sent: 14 April 2008 12:50
To: [hidden email]
Subject: Manual upgrading - Was: Re: Problems reading LSM files

> Hi Carlos, Michael and Wayne,
>
> Thank you for your help. Unfortunately I wasn't able to update to version
> 1.40. The update feature was "Unable to open release notes at
> http://rsb.info.nih.gov/ij/notes.html" and didn't update the software. On
> the ImageJ web-page I only found version 1.39.

You can always upgrade using the good old JAR download method described on

http://rsb.info.nih.gov/ij/upgrade/

which means "manually" copying the new ij.jar to the the ImageJ folder.

(However, the new (built-in) plugin makes things soo much easier - if your
version if new enough to use it)

Joachim

______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email
______________________________________________________________________